├── .gitignore ├── Examples ├── FASTA │ └── sequences.fasta └── Results_3DFI │ ├── FASTA │ ├── ECU03_1140.fasta │ ├── ECU06_1350.fasta │ └── ECU08_1425.fasta │ ├── Folding │ ├── ALPHAFOLD_3D_Parsed │ │ ├── ECU03_1140-m1.pdb │ │ ├── ECU03_1140-m2.pdb │ │ ├── ECU03_1140-m3.pdb │ │ ├── ECU03_1140-m4.pdb │ │ ├── ECU03_1140-m5.pdb │ │ ├── ECU06_1350-m1.pdb │ │ ├── ECU06_1350-m2.pdb │ │ ├── ECU06_1350-m3.pdb │ │ ├── ECU06_1350-m4.pdb │ │ ├── ECU06_1350-m5.pdb │ │ ├── ECU08_1425-m1.pdb │ │ ├── ECU08_1425-m2.pdb │ │ ├── ECU08_1425-m3.pdb │ │ ├── ECU08_1425-m4.pdb │ │ └── ECU08_1425-m5.pdb │ ├── RAPTORX_3D │ │ ├── CNFPRED │ │ │ ├── ECU03_1140-2pi2A.cnfpred │ │ │ ├── ECU03_1140-3kdfB.cnfpred │ │ │ ├── ECU03_1140-3kf6A.cnfpred │ │ │ ├── ECU03_1140-4gnxB.cnfpred │ │ │ ├── ECU03_1140-4joiA.cnfpred │ │ │ ├── ECU06_1350-2vk3A.cnfpred │ │ │ ├── ECU06_1350-3h20A.cnfpred │ │ │ ├── ECU06_1350-4qwoA.cnfpred │ │ │ ├── ECU06_1350-5zzaP.cnfpred │ │ │ ├── ECU06_1350-6iqkA.cnfpred │ │ │ ├── ECU08_1425-1l1oA.cnfpred │ │ │ ├── ECU08_1425-2pi2E.cnfpred │ │ │ ├── ECU08_1425-3kf6B.cnfpred │ │ │ ├── ECU08_1425-4gnxA.cnfpred │ │ │ └── ECU08_1425-4joiC.cnfpred │ │ ├── FASTA_ALN │ │ │ ├── ECU03_1140-2pi2A.fasta │ │ │ ├── ECU03_1140-3kdfB.fasta │ │ │ ├── ECU03_1140-3kf6A.fasta │ │ │ ├── ECU03_1140-4gnxB.fasta │ │ │ ├── ECU03_1140-4joiA.fasta │ │ │ ├── ECU06_1350-2vk3A.fasta │ │ │ ├── ECU06_1350-3h20A.fasta │ │ │ ├── ECU06_1350-4qwoA.fasta │ │ │ ├── ECU06_1350-5zzaP.fasta │ │ │ ├── ECU06_1350-6iqkA.fasta │ │ │ ├── ECU08_1425-1l1oA.fasta │ │ │ ├── ECU08_1425-2pi2E.fasta │ │ │ ├── ECU08_1425-3kf6B.fasta │ │ │ ├── ECU08_1425-4gnxA.fasta │ │ │ └── ECU08_1425-4joiC.fasta │ │ ├── PDB │ │ │ ├── ECU03_1140-m1.pdb │ │ │ ├── ECU03_1140-m2.pdb │ │ │ ├── ECU03_1140-m3.pdb │ │ │ ├── ECU03_1140-m4.pdb │ │ │ ├── ECU03_1140-m5.pdb │ │ │ ├── ECU06_1350-m1.pdb │ │ │ ├── ECU06_1350-m2.pdb │ │ │ ├── ECU06_1350-m3.pdb │ │ │ ├── ECU06_1350-m4.pdb │ │ │ ├── ECU06_1350-m5.pdb │ │ │ ├── ECU08_1425-m1.pdb │ │ │ ├── ECU08_1425-m2.pdb │ │ │ ├── ECU08_1425-m3.pdb │ │ │ ├── ECU08_1425-m4.pdb │ │ │ └── ECU08_1425-m5.pdb │ │ ├── RANK │ │ │ ├── ECU03_1140.rank │ │ │ ├── ECU06_1350.rank │ │ │ └── ECU08_1425.rank │ │ ├── TGT │ │ │ ├── ECU03_1140.tgt │ │ │ ├── ECU06_1350.tgt │ │ │ └── ECU08_1425.tgt │ │ └── raptorx.log │ └── ROSETTAFOLD_3D_Parsed │ │ ├── ECU03_1140-m1.pdb │ │ ├── ECU06_1350-m1.pdb │ │ └── ECU08_1425-m1.pdb │ ├── Homology │ ├── GESAMT │ │ ├── ALPHAFOLD │ │ │ ├── ECU03_1140-m1.normal.gesamt.gz │ │ │ ├── ECU03_1140-m2.normal.gesamt.gz │ │ │ ├── ECU03_1140-m3.normal.gesamt.gz │ │ │ ├── ECU03_1140-m4.normal.gesamt.gz │ │ │ ├── ECU03_1140-m5.normal.gesamt.gz │ │ │ ├── ECU06_1350-m1.normal.gesamt.gz │ │ │ ├── ECU06_1350-m2.normal.gesamt.gz │ │ │ ├── ECU06_1350-m3.normal.gesamt.gz │ │ │ ├── ECU06_1350-m4.normal.gesamt.gz │ │ │ ├── ECU06_1350-m5.normal.gesamt.gz │ │ │ ├── ECU08_1425-m1.normal.gesamt.gz │ │ │ ├── ECU08_1425-m2.normal.gesamt.gz │ │ │ ├── ECU08_1425-m3.normal.gesamt.gz │ │ │ ├── ECU08_1425-m4.normal.gesamt.gz │ │ │ └── ECU08_1425-m5.normal.gesamt.gz │ │ ├── ALPHAFOLD_GESAMT_per_model.matches │ │ ├── ALPHAFOLD_GESAMT_per_protein.matches │ │ ├── All_GESAMT_matches_per_protein.tsv │ │ ├── RAPTORX │ │ │ ├── ECU03_1140-m1.normal.gesamt.gz │ │ │ ├── ECU03_1140-m2.normal.gesamt.gz │ │ │ ├── ECU03_1140-m3.normal.gesamt.gz │ │ │ ├── ECU03_1140-m4.normal.gesamt.gz │ │ │ ├── ECU03_1140-m5.normal.gesamt.gz │ │ │ ├── ECU06_1350-m1.normal.gesamt.gz │ │ │ ├── ECU06_1350-m2.normal.gesamt.gz │ │ │ ├── ECU06_1350-m3.normal.gesamt.gz │ │ │ ├── ECU06_1350-m4.normal.gesamt.gz │ │ │ ├── ECU06_1350-m5.normal.gesamt.gz │ │ │ ├── ECU08_1425-m1.normal.gesamt.gz │ │ │ ├── ECU08_1425-m2.normal.gesamt.gz │ │ │ ├── ECU08_1425-m3.normal.gesamt.gz │ │ │ ├── ECU08_1425-m4.normal.gesamt.gz │ │ │ └── ECU08_1425-m5.normal.gesamt.gz │ │ ├── RAPTORX_GESAMT_per_model.matches │ │ ├── RAPTORX_GESAMT_per_protein.matches │ │ ├── ROSETTAFOLD │ │ │ ├── ECU03_1140-m1.normal.gesamt.gz │ │ │ ├── ECU06_1350-m1.normal.gesamt.gz │ │ │ └── ECU08_1425-m1.normal.gesamt.gz │ │ ├── ROSETTAFOLD_GESAMT_per_model.matches │ │ └── ROSETTAFOLD_GESAMT_per_protein.matches │ └── LOGS │ │ ├── GESAMT_ALPHAFOLD_2021-09-15.log │ │ ├── GESAMT_ALPHAFOLD_2021-09-15_descriptive_matches.err │ │ ├── GESAMT_RAPTORX_2021-09-15.log │ │ ├── GESAMT_RAPTORX_2021-09-15_descriptive_matches.err │ │ ├── GESAMT_ROSETTAFOLD_2021-09-15.log │ │ └── GESAMT_ROSETTAFOLD_2021-09-15_descriptive_matches.err │ └── Visualization │ ├── ALPHAFOLD │ ├── ECU03_1140-m1 │ │ ├── ECU03_1140-m1.pdb │ │ ├── ECU03_1140-m1_1quq_C.cxs │ │ ├── ECU03_1140-m1_2pqa_A.cxs │ │ ├── ECU03_1140-m1_3kdf_B.cxs │ │ ├── ECU03_1140-m1_3kdf_D.cxs │ │ └── ECU03_1140-m1_4gnx_B.cxs │ ├── ECU03_1140-m2 │ │ ├── ECU03_1140-m2.pdb │ │ ├── ECU03_1140-m2_1quq_C.cxs │ │ ├── ECU03_1140-m2_2pqa_A.cxs │ │ ├── ECU03_1140-m2_3kdf_D.cxs │ │ ├── ECU03_1140-m2_4gnx_B.cxs │ │ └── ECU03_1140-m2_4gop_B.cxs │ ├── ECU03_1140-m3 │ │ ├── ECU03_1140-m3.pdb │ │ ├── ECU03_1140-m3_1quq_C.cxs │ │ ├── ECU03_1140-m3_2pqa_A.cxs │ │ ├── ECU03_1140-m3_3kdf_B.cxs │ │ ├── ECU03_1140-m3_3kdf_D.cxs │ │ └── ECU03_1140-m3_4gnx_B.cxs │ ├── ECU03_1140-m4 │ │ ├── ECU03_1140-m4.pdb │ │ ├── ECU03_1140-m4_1quq_C.cxs │ │ ├── ECU03_1140-m4_2pqa_A.cxs │ │ ├── ECU03_1140-m4_3kdf_B.cxs │ │ ├── ECU03_1140-m4_3kdf_D.cxs │ │ └── ECU03_1140-m4_4gnx_B.cxs │ ├── ECU03_1140-m5 │ │ ├── ECU03_1140-m5.pdb │ │ ├── ECU03_1140-m5_1quq_C.cxs │ │ ├── ECU03_1140-m5_2pqa_A.cxs │ │ ├── ECU03_1140-m5_3kdf_B.cxs │ │ ├── ECU03_1140-m5_3kdf_D.cxs │ │ └── ECU03_1140-m5_4gnx_B.cxs │ ├── ECU06_1350-m1 │ │ ├── ECU06_1350-m1.pdb │ │ ├── ECU06_1350-m1_1ypr_A.cxs │ │ ├── ECU06_1350-m1_3d9y_A.cxs │ │ ├── ECU06_1350-m1_3d9y_B.cxs │ │ ├── ECU06_1350-m1_3dav_B.cxs │ │ └── ECU06_1350-m1_5yed_A.cxs │ ├── ECU06_1350-m2 │ │ ├── ECU06_1350-m2.pdb │ │ ├── ECU06_1350-m2_3d9y_A.cxs │ │ ├── ECU06_1350-m2_3d9y_B.cxs │ │ ├── ECU06_1350-m2_3dav_B.cxs │ │ ├── ECU06_1350-m2_5yed_A.cxs │ │ └── ECU06_1350-m2_5yee_A.cxs │ ├── ECU06_1350-m3 │ │ ├── ECU06_1350-m3.pdb │ │ ├── ECU06_1350-m3_3d9y_B.cxs │ │ ├── ECU06_1350-m3_3dav_A.cxs │ │ ├── ECU06_1350-m3_3dav_B.cxs │ │ ├── ECU06_1350-m3_4qwo_B.cxs │ │ └── ECU06_1350-m3_5zza_P.cxs │ ├── ECU06_1350-m4 │ │ ├── ECU06_1350-m4.pdb │ │ ├── ECU06_1350-m4_3d9y_A.cxs │ │ ├── ECU06_1350-m4_3d9y_B.cxs │ │ ├── ECU06_1350-m4_3dav_B.cxs │ │ ├── ECU06_1350-m4_4qwo_B.cxs │ │ └── ECU06_1350-m4_5zza_P.cxs │ ├── ECU06_1350-m5 │ │ ├── ECU06_1350-m5.pdb │ │ ├── ECU06_1350-m5_1ypr_A.cxs │ │ ├── ECU06_1350-m5_3d9y_A.cxs │ │ ├── ECU06_1350-m5_3d9y_B.cxs │ │ ├── ECU06_1350-m5_3dav_A.cxs │ │ └── ECU06_1350-m5_3dav_B.cxs │ ├── ECU08_1425-m1 │ │ ├── ECU08_1425-m1.pdb │ │ ├── ECU08_1425-m1_3k0x_A.cxs │ │ ├── ECU08_1425-m1_3kf6_B.cxs │ │ ├── ECU08_1425-m1_5doi_F.cxs │ │ ├── ECU08_1425-m1_5doi_G.cxs │ │ └── ECU08_1425-m1_5doi_H.cxs │ ├── ECU08_1425-m2 │ │ ├── ECU08_1425-m2.pdb │ │ ├── ECU08_1425-m2_3k0x_A.cxs │ │ ├── ECU08_1425-m2_3kf6_B.cxs │ │ ├── ECU08_1425-m2_5doi_F.cxs │ │ ├── ECU08_1425-m2_5doi_G.cxs │ │ └── ECU08_1425-m2_5doi_H.cxs │ ├── ECU08_1425-m3 │ │ ├── ECU08_1425-m3.pdb │ │ ├── ECU08_1425-m3_3k0x_A.cxs │ │ ├── ECU08_1425-m3_3kf6_B.cxs │ │ ├── ECU08_1425-m3_5doi_F.cxs │ │ ├── ECU08_1425-m3_5doi_G.cxs │ │ └── ECU08_1425-m3_5doi_H.cxs │ ├── ECU08_1425-m4 │ │ ├── ECU08_1425-m4.pdb │ │ ├── ECU08_1425-m4_3k0x_A.cxs │ │ ├── ECU08_1425-m4_3kf6_B.cxs │ │ ├── ECU08_1425-m4_5doi_F.cxs │ │ ├── ECU08_1425-m4_5doi_G.cxs │ │ └── ECU08_1425-m4_5doi_H.cxs │ └── ECU08_1425-m5 │ │ ├── ECU08_1425-m5.pdb │ │ ├── ECU08_1425-m5_3k0x_A.cxs │ │ ├── ECU08_1425-m5_3kf6_B.cxs │ │ ├── ECU08_1425-m5_5doi_F.cxs │ │ ├── ECU08_1425-m5_5doi_G.cxs │ │ └── ECU08_1425-m5_5doi_H.cxs │ ├── RAPTORX │ ├── ECU03_1140-m1 │ │ ├── ECU03_1140-m1.pdb │ │ ├── ECU03_1140-m1_1quq_C.cxs │ │ ├── ECU03_1140-m1_3kdf_B.cxs │ │ ├── ECU03_1140-m1_3kdf_D.cxs │ │ ├── ECU03_1140-m1_3kf6_A.cxs │ │ └── ECU03_1140-m1_4gnx_B.cxs │ ├── ECU03_1140-m2 │ │ ├── ECU03_1140-m2.pdb │ │ ├── ECU03_1140-m2_1quq_C.cxs │ │ ├── ECU03_1140-m2_3kdf_B.cxs │ │ ├── ECU03_1140-m2_3kdf_D.cxs │ │ ├── ECU03_1140-m2_4gnx_B.cxs │ │ └── ECU03_1140-m2_4joi_A.cxs │ ├── ECU03_1140-m3 │ │ ├── ECU03_1140-m3.pdb │ │ ├── ECU03_1140-m3_1l1o_B.cxs │ │ ├── ECU03_1140-m3_1l1o_E.cxs │ │ ├── ECU03_1140-m3_2pi2_B.cxs │ │ ├── ECU03_1140-m3_2pi2_D.cxs │ │ └── ECU03_1140-m3_3kdf_B.cxs │ ├── ECU03_1140-m4 │ │ ├── ECU03_1140-m4.pdb │ │ ├── ECU03_1140-m4_1l1o_E.cxs │ │ ├── ECU03_1140-m4_1quq_A.cxs │ │ ├── ECU03_1140-m4_2pi2_D.cxs │ │ ├── ECU03_1140-m4_3kdf_B.cxs │ │ └── ECU03_1140-m4_3kdf_D.cxs │ ├── ECU03_1140-m5 │ │ ├── ECU03_1140-m5.pdb │ │ ├── ECU03_1140-m5_3kdf_B.cxs │ │ ├── ECU03_1140-m5_4gnx_B.cxs │ │ ├── ECU03_1140-m5_4gnx_Y.cxs │ │ ├── ECU03_1140-m5_4gop_B.cxs │ │ └── ECU03_1140-m5_4gop_Y.cxs │ ├── ECU06_1350-m1 │ │ ├── ECU06_1350-m1.pdb │ │ ├── ECU06_1350-m1_1hlu_P.cxs │ │ ├── ECU06_1350-m1_1pne_A.cxs │ │ ├── ECU06_1350-m1_2v8c_A.cxs │ │ ├── ECU06_1350-m1_2v8f_A.cxs │ │ └── ECU06_1350-m1_2vk3_A.cxs │ ├── ECU06_1350-m2 │ │ ├── ECU06_1350-m2.pdb │ │ ├── ECU06_1350-m2_3d9y_B.cxs │ │ ├── ECU06_1350-m2_3dav_B.cxs │ │ ├── ECU06_1350-m2_5yed_A.cxs │ │ ├── ECU06_1350-m2_5zza_P.cxs │ │ └── ECU06_1350-m2_5zzb_A.cxs │ ├── ECU06_1350-m3 │ │ ├── ECU06_1350-m3.pdb │ │ ├── ECU06_1350-m3_1cf0_B.cxs │ │ ├── ECU06_1350-m3_1cjf_A.cxs │ │ ├── ECU06_1350-m3_3ub5_P.cxs │ │ ├── ECU06_1350-m3_4qwo_A.cxs │ │ └── ECU06_1350-m3_4qwo_B.cxs │ ├── ECU06_1350-m4 │ │ ├── ECU06_1350-m4.pdb │ │ ├── ECU06_1350-m4_3h25_A.cxs │ │ ├── ECU06_1350-m4_6zp9_A.cxs │ │ └── ECU06_1350-m4_6zp9_B.cxs │ ├── ECU06_1350-m5 │ │ ├── ECU06_1350-m5.pdb │ │ ├── ECU06_1350-m5_1a0k_A.cxs │ │ ├── ECU06_1350-m5_6iqi_A.cxs │ │ ├── ECU06_1350-m5_6iqi_B.cxs │ │ ├── ECU06_1350-m5_6iqk_C.cxs │ │ └── ECU06_1350-m5_6iqk_G.cxs │ ├── ECU08_1425-m1 │ │ ├── ECU08_1425-m1.pdb │ │ ├── ECU08_1425-m1_3k0x_A.cxs │ │ ├── ECU08_1425-m1_3kf6_B.cxs │ │ ├── ECU08_1425-m1_4joi_C.cxs │ │ ├── ECU08_1425-m1_4joi_D.cxs │ │ └── ECU08_1425-m1_6w6w_D.cxs │ ├── ECU08_1425-m2 │ │ ├── ECU08_1425-m2.pdb │ │ ├── ECU08_1425-m2_3k0x_A.cxs │ │ ├── ECU08_1425-m2_3kf6_B.cxs │ │ ├── ECU08_1425-m2_5doi_E.cxs │ │ ├── ECU08_1425-m2_5doi_F.cxs │ │ └── ECU08_1425-m2_5doi_G.cxs │ ├── ECU08_1425-m3 │ │ ├── ECU08_1425-m3.pdb │ │ ├── ECU08_1425-m3_1l1o_D.cxs │ │ ├── ECU08_1425-m3_1quq_B.cxs │ │ ├── ECU08_1425-m3_2pqa_B.cxs │ │ ├── ECU08_1425-m3_2pqa_D.cxs │ │ └── ECU08_1425-m3_3kdf_A.cxs │ ├── ECU08_1425-m4 │ │ ├── ECU08_1425-m4.pdb │ │ ├── ECU08_1425-m4_1l1o_A.cxs │ │ ├── ECU08_1425-m4_1l1o_D.cxs │ │ ├── ECU08_1425-m4_1quq_B.cxs │ │ ├── ECU08_1425-m4_2pqa_D.cxs │ │ └── ECU08_1425-m4_3kdf_A.cxs │ └── ECU08_1425-m5 │ │ ├── ECU08_1425-m5.pdb │ │ ├── ECU08_1425-m5_2pqa_D.cxs │ │ ├── ECU08_1425-m5_4gnx_A.cxs │ │ ├── ECU08_1425-m5_4gnx_X.cxs │ │ ├── ECU08_1425-m5_4gop_A.cxs │ │ └── ECU08_1425-m5_4gop_X.cxs │ ├── ROSETTAFOLD │ ├── ECU03_1140-m1 │ │ ├── ECU03_1140-m1.pdb │ │ ├── ECU03_1140-m1_1quq_A.cxs │ │ ├── ECU03_1140-m1_1quq_C.cxs │ │ ├── ECU03_1140-m1_3kdf_B.cxs │ │ ├── ECU03_1140-m1_3kdf_D.cxs │ │ └── ECU03_1140-m1_4gnx_B.cxs │ ├── ECU06_1350-m1 │ │ ├── ECU06_1350-m1.pdb │ │ ├── ECU06_1350-m1_1ypr_A.cxs │ │ ├── ECU06_1350-m1_1ypr_B.cxs │ │ ├── ECU06_1350-m1_4qwo_A.cxs │ │ ├── ECU06_1350-m1_4qwo_B.cxs │ │ └── ECU06_1350-m1_5zza_P.cxs │ └── ECU08_1425-m1 │ │ ├── ECU08_1425-m1.pdb │ │ ├── ECU08_1425-m1_3k0x_A.cxs │ │ ├── ECU08_1425-m1_5doi_E.cxs │ │ ├── ECU08_1425-m1_5doi_F.cxs │ │ ├── ECU08_1425-m1_5doi_G.cxs │ │ └── ECU08_1425-m1_5doi_H.cxs │ └── predicted_structures.log ├── Homology_search ├── PDB_headers.pl ├── descriptive_matches.pl ├── parse_all_models_by_Q.pl ├── run_GESAMT.pl ├── run_MICAN_on_homology_results.pl ├── run_foldseek.pl └── update_PDB.pl ├── Images ├── Bad_Match.png ├── Bad_Predicted_Fold.png ├── ECU03_1140-m4.png ├── ECU03_1140-m4_3kdf_B.png ├── Good_Match.png ├── Good_Match_Bad_Fold.png ├── Just_PDB.png ├── Just_PDB_rainbow.png ├── Logo.png ├── With_Alignment.png ├── bfactor.png ├── bfactor_key.png ├── bfactor_key_cmd.png └── no_homology.png ├── LICENSE ├── Misc_tools ├── rename_files.pl ├── split_Fasta.pl └── split_PDB.pl ├── Notes └── Installation_notes.sh ├── Prediction ├── AlphaFold2 │ ├── alphafold.pl │ ├── get_pLDDTs.pl │ └── parse_af_results.pl ├── RaptorX │ └── raptorx.pl ├── RoseTTAFold │ ├── install_pyrosetta.sh │ ├── parse_rf_results.pl │ └── rosettafold.pl ├── trRosetta │ ├── create_npz.pl │ ├── create_pdb.pl │ ├── fasta_oneliner.pl │ ├── run_hhblits.pl │ ├── sanitize_pdb.pl │ └── trRosetta_installation_notes.sh └── trRosetta2 │ ├── fasta_oneliner.pl │ ├── parse_tr2_results.pl │ └── trRosetta2.pl ├── README.md ├── Visualization ├── Helper_Scripts │ ├── chimerax_session_creator.py │ ├── color_alphafold.py │ ├── color_rosettafold.py │ └── restore_chimerax_session.py ├── inspect_3D_structures.pl └── prepare_visualizations.pl ├── create_3DFI_db.pl ├── run_3DFI.pl ├── run_visualizations.pl └── setup_3DFI.pl /.gitignore: -------------------------------------------------------------------------------- 1 | 2 | .DS_Store 3 | 3D/ 4 | Homology_Tools/ -------------------------------------------------------------------------------- /Examples/FASTA/sequences.fasta: -------------------------------------------------------------------------------- 1 | >ECU03_1140-t26_1-p1 | transcript=ECU03_1140-t26_1 | gene=ECU03_1140 | organism=Encephalitozoon_cuniculi_GB-M1 | gene_product=hypothetical protein | transcript_product=hypothetical protein | location=AL590443:136975-137328(+) | protein_length=117 | sequence_SO=chromosome | SO=protein_coding | is_pseudo=false 2 | MTSRVGPPLRILSDSLKKLRRVSGAIFYGRREVSHVEIAGTCIDRGRVFARILDFCGEVL 3 | VEIGDQKIALGSSYLLVCKVQARSGGIGLHCKSAKRLGIFEEMFFWAEAVNLEGGLQ 4 | >ECU08_1425-t26_1-p1 | transcript=ECU08_1425-t26_1 | gene=ECU08_1425 | organism=Encephalitozoon_cuniculi_GB-M1 | gene_product=unspecified product | transcript_product=unspecified product | location=AL590448:159723-160001(-) | protein_length=92 | sequence_SO=chromosome | SO=protein_coding | is_pseudo=false 5 | MLRLLDIPVEGRTVYSFGKVRDKLENGKYEVSFREKTIIITTDRRLSIGSWIRMYGTFKS 6 | GVLRTIFVGELDGVDINLLEKAVRYVACRRKI 7 | >ECU06_1350-t26_1-p1 | transcript=ECU06_1350-t26_1 | gene=ECU06_1350 | organism=Encephalitozoon_cuniculi_GB-M1 | gene_product=hypothetical protein | transcript_product=hypothetical protein | location=AL590446:173094-173537(+) | protein_length=147 | sequence_SO=chromosome | SO=protein_coding | is_pseudo=false 8 | MPGIIYEGKGTNMEYADVFDSLVGDLKDDVLSLQLTNFDDVNHSYKSDGKCSMSVKDFDG 9 | YAENMPVKNVEYNGQKYIFMRSISDDAQPSQVFISVDGDERGRKRGMLITSFCGILRMIS 10 | TFDYQIANSVTAKIFKVLGEYSCEEEE 11 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/FASTA/ECU03_1140.fasta: -------------------------------------------------------------------------------- 1 | >ECU03_1140 2 | MTSRVGPPLRILSDSLKKLRRVSGAIFYGRREVSHVEIAGTCIDRGRVFARILDFCGEVL 3 | VEIGDQKIALGSSYLLVCKVQARSGGIGLHCKSAKRLGIFEEMFFWAEAVNLEGGLQ 4 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/FASTA/ECU06_1350.fasta: -------------------------------------------------------------------------------- 1 | >ECU06_1350 2 | MPGIIYEGKGTNMEYADVFDSLVGDLKDDVLSLQLTNFDDVNHSYKSDGKCSMSVKDFDG 3 | YAENMPVKNVEYNGQKYIFMRSISDDAQPSQVFISVDGDERGRKRGMLITSFCGILRMIS 4 | TFDYQIANSVTAKIFKVLGEYSCEEEE 5 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/FASTA/ECU08_1425.fasta: -------------------------------------------------------------------------------- 1 | >ECU08_1425 2 | MLRLLDIPVEGRTVYSFGKVRDKLENGKYEVSFREKTIIITTDRRLSIGSWIRMYGTFKS 3 | GVLRTIFVGELDGVDINLLEKAVRYVACRRKI 4 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/CNFPRED/ECU03_1140-2pi2A.cnfpred: -------------------------------------------------------------------------------- 1 | 2 | T sse_real EECCHHHHHHCEEECCEEEECCEEECEEEEEEEEEEEEECCC-EEEEEEECCCCCCEEEEEECC-------C-CCCCCC 3 | T acc_real BMBMBMMBEEBEEMEEMMMMEMBMBMMBMBBBBBMEMEEMEE-MBMBEBMMEMMEMBMBMMEME-------E-EMMEEE 4 | T 2pi2A 47 VPCTISQLLSATLVDEVFRIGNVEISQVTIVGIIRHAEKAPT-NIVYKIDDMTAAPMDVRQWVDTDDTSSEN-TVVPPE 123 (270) 5 | *+*+*********+*~**++*~*+||+|||||||||* -**++++++ .~**++|+* -***~~ 6 | S ECU03_1140 9 LRILSDSLKKLRRVSGAIFYGRREVSHVEIAGTCIDR-----GRVFARILDF-CGEVLVEIG----------DQKIALG 71 (117) 7 | S acc_pred BMBBMEMBEEBMEMEEBBBBEEMMBMMBMBBBBBBMM-----EEMBBMBBMB-BBMBMBMMM----------EEEMEEE 8 | S acc_conf 6584474667855444467555556558668768846-----5857869867-766848554----------7874447 9 | S sse_pred EEEECHHHCCEEEECCEEEECCEEEEEEEEEEEEEEC-----CCCEEEEEEE-CEEEEEEEC----------CEEEECC 10 | S sse_conf 6667453334588567899766788799999899975-----9958999886-468999977----------7566658 11 | 12 | 13 | T sse_real CEEEEEEEEEEECCEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHH 14 | T acc_real MMBMBBBMBMMEEEEMMBMBMEMEMMEEMEMMEMBEEEBEEMMEEMM 15 | T 2pi2A 124 TYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLS 170 (270) 16 | ***++|++||++~~**||+*+***~******** -*++********* 17 | S ECU03_1140 72 SSYLLVCKVQARSGGIGLHCKSAKRLGIFEEMF-FWAEAVNLEGGLQ 117 (117) 18 | S acc_pred EMBBBMBMBBBMEEMBBBBBEMBEMBMBBBBBB-BBBBBMEMEEEME 19 | S acc_conf 556585858675754868585474574775687-7695857478549 20 | S sse_pred CEEEEEEEEEECCCEEEEEECCCEEEEEHHHHH-HHHHHHHHCCCCC 21 | S sse_conf 759999999966888999975554653455677-8997764545679 22 | 23 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/CNFPRED/ECU03_1140-3kdfB.cnfpred: -------------------------------------------------------------------------------- 1 | 2 | T sse_real CEECCHHHHHCCEEECCEEEECCEEECEEEEEEEEEEEEECCC-EEEEEEECCCCCCEEEEEEC----------CCCCC 3 | T acc_real MBMBMBMMBMEBEMEEEMMMMEEBEBEMBMBBBBBMEMEEMEE-MBMBMBMMEMMEMBMBMMEE----------EMBEE 4 | T 3kdfB 6 IVPCTISQLLSATLVDEVFRIGNVEISQVTIVGIIRHAEKAPT-NIVYKIDDMTAAPMDVRQWVDTDDTSSEN-TVVPP 82 (132) 5 | ****+*********+~~**++*~*+|++|||||||||* -**++++++ .~**++|*+ -***~ 6 | S ECU03_1140 8 PLRILSDSLKKLRRVSGAIFYGRREVSHVEIAGTCIDR-----GRVFARILDF-CGEVLVEIG----------DQKIAL 70 (117) 7 | S acc_pred BBMBBMEMBEEBMEMEEBBBBEEMMBMMBMBBBBBBMM-----EEMBBMBBMB-BBMBMBMMM----------EEEMEE 8 | S acc_conf 36584474667855444467555556558668768846-----5857869867-766848554----------787444 9 | S sse_pred CEEEECHHHCCEEEECCEEEECCEEEEEEEEEEEEEEC-----CCCEEEEEEE-CEEEEEEEC----------CEEEEC 10 | S sse_conf 76667453334588567899766788799999899975-----9958999886-468999977----------756665 11 | 12 | 13 | T sse_real CCEEEEEEEEEEECCEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHC 14 | T acc_real EMMBMBBBEBEMEEEEMMBMBEMMEEMEEEEMMEMBEEMBEEMMEEEM 15 | T 3kdfB 83 ETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLS 130 (132) 16 | ~~**++|++|+**~~**||++++****** -******+++******** 17 | S ECU03_1140 71 GSSYLLVCKVQARSGGIGLHCKSAKRLGI-FEEMFFWAEAVNLEGGLQ 117 (117) 18 | S acc_pred EEMBBBMBMBBBMEEMBBBBBEMBEMBMB-BBBBBBBBBBMEMEEEME 19 | S acc_conf 75565858586757548685854745747-756877695857478549 20 | S sse_pred CCEEEEEEEEEECCCEEEEEECCCEEEEE-HHHHHHHHHHHHHCCCCC 21 | S sse_conf 87599999999668889999755546534-556778997764545679 22 | 23 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/CNFPRED/ECU03_1140-3kf6A.cnfpred: -------------------------------------------------------------------------------- 1 | 2 | T sse_real CCCCHHHHCCCCCCCC----CCEEECCEEECEEEEEEEEEEEEEECCEEEEEEECCCCCEEEEEEECCCCHHHHHHHCC 3 | T acc_real BBBMBMBBMEBEMEEE----EEBMBMEMEBMMBBBBBMBEMMMEMEEMMBBMBMBEMEEMBMBBBMMEEMEEBBEMBME 4 | T 3kf6A 19 NPMFISDVHKISFHPHLQR-YIGFWMGFPIRWIQIVGYIAAIDIYEGKHVLTVDDCSGMVLRVVFIIQDDFSMSKRAIS 96 (159) 5 | *+*+**+***++** -**||+*~*||+||||||||+* .~+*++++++ -*++|+|+*~ .~ 6 | S ECU03_1140 9 LRILSDSLKKLRRV-----SGAIFYGRREVSHVEIAGTCIDR----GRVFARILDF---CGEVLVEIGD--------QK 67 (117) 7 | S acc_pred BMBBMEMBEEBMEM-----EEBBBBEEMMBMMBMBBBBBBMM----EEMBBMBBMB---BBMBMBMMME--------EE 8 | S acc_conf 65844746678554-----44467555556558668768846----5857869867---7668485547--------87 9 | S sse_pred EEEECHHHCCEEEE-----CCEEEECCEEEEEEEEEEEEEEC----CCCEEEEEEE---CEEEEEEECC--------EE 10 | S sse_conf 66674533345885-----67899766788799999899975----9958999886---4689999777--------56 11 | 12 | 13 | T sse_real CCCCCEEEEEEEEECCCCCCEEEEEEEEEECCCHHHHHHHHHHHHHHHHHH 14 | T acc_real MEEEMMBBBMBMBMMEEEEBMBBMEEBEMMEEEEMMEEBMEEBEEMMEEMM 15 | T 3kf6A 97 MSPGNVVCVFGKINSFRSEVELIAQSFEELRDPNDEWKAWQKRMRYKKNLT 147 (159) 16 | **~~***+||++||+*..**+|++*+***** -**|+**+++++*++**+* 17 | S ECU03_1140 68 IALGSSYLLVCKVQARSGGIGLHCKSAKRLG-IFEEMFFWAEAVNLEGGLQ 117 (117) 18 | S acc_pred MEEEEMBBBMBMBBBMEEMBBBBBEMBEMBM-BBBBBBBBBBBMEMEEEME 19 | S acc_conf 4447556585858675754868585474574-7756877695857478549 20 | S sse_pred EECCCEEEEEEEEEECCCEEEEEECCCEEEE-EHHHHHHHHHHHHHCCCCC 21 | S sse_conf 6658759999999966888999975554653-4556778997764545679 22 | 23 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/CNFPRED/ECU03_1140-4gnxB.cnfpred: -------------------------------------------------------------------------------- 1 | 2 | T sse_real CCEECCEECCEEEEEEEEEEEEECCC-EEEEEEECCCCEEEEEEECC--------C-CCCCCCCEEEEEEEEEEECCEE 3 | T acc_real EBMBMEMEBMEBBBBBBBEEMEEEEE-BBMBMBMBEMMEBMBMMEEE--------E-EEBEEEMMBMBMBMBEMMEEEM 4 | T 4gnxB 28 EFILDGAELGQLTFVAVVRNISRNAT-NVAYSVEDGTGQIEVRQWLDSSSDDSSKA-SEIRNNVYVRVLGTLKSFQNRR 104 (136) 5 | **+***~*|+*+|||||||+* -***+++++~~*+|||+* -***~~~**+++++|+*+~~*+ 6 | S ECU03_1140 25 AIFYGRREVSHVEIAGTCIDR-----GRVFARILDFCGEVLVEIG-----------DQKIALGSSYLLVCKVQARSGGI 87 (117) 7 | S acc_pred BBBBEEMMBMMBMBBBBBBMM-----EEMBBMBBMBBBMBMBMMM-----------EEEMEEEEMBBBMBMBBBMEEMB 8 | S acc_conf 467555556558668768846-----5857869867766848554-----------78744475565858586757548 9 | S sse_pred EEEECCEEEEEEEEEEEEEEC-----CCCEEEEEEECEEEEEEEC-----------CEEEECCCEEEEEEEEEECCCEE 10 | S sse_conf 899766788799999899975-----9958999886468999977-----------75666587599999999668889 11 | 12 | 13 | T sse_real EEEEEEEEECCCHHHHHHHHHHHHHHHHHHH 14 | T acc_real BBMBEEBEMMEEEEMBMEBEEMBEEMMEEME 15 | T 4gnxB 105 SISSGHMRPVIDYNEVMFHRLEAVHAHLQVT 135 (136) 16 | ||+++****** -****+**+++******** 17 | S ECU03_1140 88 GLHCKSAKRLG-IFEEMFFWAEAVNLEGGLQ 117 (117) 18 | S acc_pred BBBBEMBEMBM-BBBBBBBBBBBMEMEEEME 19 | S acc_conf 68585474574-7756877695857478549 20 | S sse_pred EEEECCCEEEE-EHHHHHHHHHHHHHCCCCC 21 | S sse_conf 99975554653-4556778997764545679 22 | 23 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/CNFPRED/ECU03_1140-4joiA.cnfpred: -------------------------------------------------------------------------------- 1 | 2 | T sse_real EECCHHHHHHCEECCCCCCCEEECCEEECEEEEEEEEEEEEECCC-EEEEEEECCCCEEEEEEECCC------------ 3 | T acc_real MMBMBMMBMEBEEMEEEEMMBMMEEBEBMMBBBBBMBEMMEEEEE-MMBBBBMMEMMEBMBBBEMEE------------ 4 | T 4joiA 9 AKLYIRDILDMKESRQVPGVFLYNGHPIKQVDVLGTVIGVRERDA-FYSYGVDDSTGVINCICWKKLNTESVSAAPSAA 86 (166) 5 | ++++******++** .*++||+~~*|++||||||||+* .*+|++|**~~**|||+* 6 | S ECU03_1140 9 LRILSDSLKKLRRV---SGAIFYGRREVSHVEIAGTCIDR-----GRVFARILDFCGEVLVEIG--------------- 64 (117) 7 | S acc_pred BMBBMEMBEEBMEM---EEBBBBEEMMBMMBMBBBBBBMM-----EEMBBMBBMBBBMBMBMMM--------------- 8 | S acc_conf 65844746678554---44467555556558668768846-----5857869867766848554--------------- 9 | S sse_pred EEEECHHHCCEEEE---CCEEEECCEEEEEEEEEEEEEEC-----CCCEEEEEEECEEEEEEEC--------------- 10 | S sse_conf 66674533345885---67899766788799999899975-----9958999886468999977--------------- 11 | 12 | 13 | T sse_real -------CCCCCCHHHHHC-CCCCCCCEEEEEEEEEEECCEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHCC 14 | T acc_real -------MEEEEEEEEEEE-EEMEEEMBBMBMBBBMEEEEEMMBMMEEMEEBEBEEEEEBEEMEEMBMEMBEEEB 15 | T 4joiA 87 RELSLTSQLKKLQETIEQK-TKIEIGDTIRVRGSIRTYREEREIHATTYYKVDDPVWNIQIARMLELPTIYRKVY 160 (166) 16 | -***~~***++|++||**~~*+||+*******+* -**+***++**++****~ 17 | S ECU03_1140 65 -------------------DQKIALGSSYLLVCKVQARSGGIGLHCKSAKRLGI---FEEMFFWAEAVNLEGGLQ 117 (117) 18 | S acc_pred -------------------EEEMEEEEMBBBMBMBBBMEEMBBBBBEMBEMBMB---BBBBBBBBBBMEMEEEME 19 | S acc_conf -------------------78744475565858586757548685854745747---756877695857478549 20 | S sse_pred -------------------CEEEECCCEEEEEEEEEECCCEEEEEECCCEEEEE---HHHHHHHHHHHHHCCCCC 21 | S sse_conf -------------------75666587599999999668889999755546534---556778997764545679 22 | 23 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/CNFPRED/ECU06_1350-2vk3A.cnfpred: -------------------------------------------------------------------------------- 1 | 2 | T sse_real HHHHHHHHHCHHHHC--CEEEEEEEECCCCC-CEEEECCCCCCCCCCHHHHHHHHCCCCCH-HHHHCEEECCEEEEEEE 3 | T acc_real EEEBMEMBMEBMEME--MBMBBBBBBBEEMM-EMMBMBEEMMBEEBMEEBBEEBMMEEMEM-BMEEMBMBMEMEBMBME 4 | T 2vk3A 3 MAGWQSYVDNLMCDG--CCQEAAIVGYCDAK-YVWAATAGGVFQSITPAEIDVIIGKDREG-FFTNGLTLGGKKCSVIR 77 (142) 5 | *+**++++|+||*** -*+++*+|++*~ -***** .~~*~**+~*++*++* -*~~*+|++**+||||| 6 | S ECU06_1350 12 NMEYADVFDSLVGDLKDDVLSLQLTNFDD--VNHSYKS--DGKCSMSVKDFDGYAE-----NMPVKNVEYNGQKYIFMR 81 (147) 7 | S acc_pred EMEMBEMBEEBBEEBEEMBBBBMBBMMEE--MEMEMEE--EMEMEEEMEMBEEMME-----EBEMEMBMMEEMEBBBBM 8 | S acc_conf 76664767766686869646565745655--4544575--7585446585745448-----766484854745467786 9 | S sse_pred CHHHHHHHHHHHHCCCCCEEEEEEEECCC--CCCCCCC--CCCCCCCECCHHHHHC-----CCCCCCEEECCEEEEEEE 10 | S sse_conf 75478989888756556558879875787--7765579--9965565445666654-----689886688898999998 11 | 12 | 13 | T sse_real EECCCCCCCEEEEEECCCCCCCCCEEEEEECCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHCCC 14 | T acc_real MMBMEEEMBBBBBMBEEEEEMMEMMBBBBBBEEBBBBBBBEEEMEMEEBMEMBMEBBEEBMEEEM 15 | T 2vk3A 78 DSLYVDSDCTMDIRTKSQGGEPTYNVAVGRAGRVLVFVMGKEGVHGGGLNKKAYSMAKYLRDSGF 142 (142) 16 | ++*~.~~*++|||||+*~~~~~****+||+**~**+++***~~~~*****++*+*++******** 17 | S ECU06_1350 82 SISDDAQPSQVFISVDGDERGRKRGMLITSFCGILRMISTFDYQIANSVTAKIFKVLGEYSCEEE 146 (147) 18 | S acc_pred BBMEEMEMBBBBBMBMEEEEEMEMBBBBBBBBEBBMBBBBBEMEMBMMBBBMBBEBBEEMEMEEE 19 | S acc_conf 35588553657774444788555646784776466567646444555478759876756645688 20 | S sse_pred ECCCCCCCEEEEEEECCCCCCCCCEEEEHEHHHHEEEEEEECCCCCCHHHHHHHHHHHCCCCCCC 21 | S sse_conf 57999986699999858989875445776566543578886565665578999998655656557 22 | 23 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/CNFPRED/ECU06_1350-3h20A.cnfpred: -------------------------------------------------------------------------------- 1 | 2 | T sse_real HHHHHHHHHHHCCCEEEEEEEECCCCCEEEE-----EEEHHHHHHCHHHHHHHHH----CCEEEEEEECC-CCCCCEEE 3 | T acc_real EEMBMEBBEBBEBEMBBBBBEMMEEMEMMEE-----EMMMEMBMEMBEMBEEBBE----EMBBBMBMBBM-EMMBBBBB 4 | T 3h20A 7 LQAIGRQLKAMGCERFDIGVRDATTGQMMNR-----EWSAAEVLQNTPWLKRMNA----QGNDVYIRPAE-QERHGLVL 75 (323) 5 | ****+*+|*++~~~+*|||||**~~~~**** -****~***++****~~~ -~*++||||+* .~~++||| 6 | S ECU06_1350 16 ADVFDSLVGDLKDDVLSLQLTNFDDVNHSYKSDGKCSMSVKDFDGYAENMPVKN-VEYNGQKYIFMRSISDDAQPSQVF 93 (147) 7 | S acc_pred BEMBEEBBEEBEEMBBBBMBBMMEEMEMEMEEEMEMEEEMEMBEEMMEEBEMEM-BMMEEMEBBBBMBBMEEMEMBBBB 8 | S acc_conf 476776668686964656574565545445757585446585745448766484-854745467786355885536577 9 | S sse_pred HHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCCCCCECCHHHHHCCCCCCC-EEECCEEEEEEEECCCCCCCEEEE 10 | S sse_conf 898988875655655887987578777655799965565445666654689886-688898999998579999866999 11 | 12 | 13 | T sse_real EEEECHHHHHHHHHC-CCCCCEEEEEECCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCC 14 | T acc_real BMEBMMEMBEEBMEE-MMMBBBBBBMMEEMMBBBBMBMEEMEMEMBBMBBEMBBEMBEBMEE 15 | T 3h20A 76 VDDLSEFDLDDMKAE-GREPALVVETSPKNYQAWVKVADAAGGELRGQIARTLASEYDADPA 136 (323) 16 | ||++**~ -*****+||+*~~~~*++*++*~~~~~**+++|++||+***~**** 17 | S ECU06_1350 94 ISVDGDE--------RGRKRGMLITSFCGILRMISTFDYQIANSVTAKIFKVLGEYSCEEEE 147 (147) 18 | S acc_pred BMBMEEE--------EEMEMBBBBBBBBEBBMBBBBBEMEMBMMBBBMBBEBBEEMEMEEEE 19 | S acc_conf 7444478--------85556467847764665676464445554787598767566456889 20 | S sse_pred EEECCCC--------CCCCCEEEEHEHHHHEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCC 21 | S sse_conf 9985898--------98754457765665435788865656655789999986556565579 22 | 23 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/CNFPRED/ECU06_1350-4qwoA.cnfpred: -------------------------------------------------------------------------------- 1 | 2 | T sse_real HHHHHHHHHHHCC--CCEEEEEEEECCCCCCEEEECCCC-CCCCCCHHHHHHHHHCCCCCCCEECCEEEEEEEEECCCC 3 | T acc_real EEBEEBBEEBEEM--EMBEBBBBBBBEEEMMMMBMMEEE-MBMEBMEEBBEMBMEMEEMEEBMBBEEEBEMMMMEBEEE 4 | T 4qwoA 26 AEWHKIIEDISKN--NKFEDAAIVDYKTTKNVLAAIPNR-TFAKINPGEVIPLITNHNILKPLIGQKFCIVYTNSLMDE 101 (157) 5 | ***++++++||** -**+++*+|++*~.~~**+* -~*~***~~+**++**~~~~*++++***+|+|++*~~.~ 6 | S ECU06_1350 13 MEYADVFDSLVGDLKDDVLSLQLTNFDDVNHSYKS----DGKCSMSVKDFDGYAENMPVKNVEYNGQKYIFMRSISDDA 87 (147) 7 | S acc_pred MEMBEMBEEBBEEBEEMBBBBMBBMMEEMEMEMEE----EMEMEEEMEMBEEMMEEBEMEMBMMEEMEBBBBMBBMEEM 8 | S acc_conf 66647677666868696465657456554544575----7585446585745448766484854745467786355885 9 | S sse_pred HHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCC----CCCCCCCECCHHHHHCCCCCCCEEECCEEEEEEEECCCCC 10 | S sse_conf 54789898887565565588798757877765579----9965565445666654689886688898999998579999 11 | 12 | 13 | T sse_real CCCEEEEEECC---CCCCEEEEEECCCEEEEEEECCCCCHHHHHHHHHHHHHHHHCCCC 14 | T acc_real EMBBBBBMBEM---EEEBMBBBBBBMMBBBBBBBMEEBMEEMBMEMBMMBBMEBMEEEM 15 | T 4qwoA 102 NTYAMELLTGY---APVSPIVIARTHTALIFLMGKPTTSRRDVYRTCRDHATRVRATGN 157 (157) 16 | ~**++|+||+* -~****+||+*****+++*+**~~~*~***+++++++*****~** 17 | S ECU06_1350 88 QPSQVFISVDGDERGRKRGMLITSFCGILRMISTFDYQIANSVTAKIFKVLGEYSCEEE 146 (147) 18 | S acc_pred EMBBBBBMBMEEEEEMEMBBBBBBBBEBBMBBBBBEMEMBMMBBBMBBEBBEEMEMEEE 19 | S acc_conf 53657774444788555646784776466567646444555478759876756645688 20 | S sse_pred CCEEEEEEECCCCCCCCCEEEEHEHHHHEEEEEEECCCCCCHHHHHHHHHHHCCCCCCC 21 | S sse_conf 86699999858989875445776566543578886565665578999998655656557 22 | 23 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/CNFPRED/ECU06_1350-5zzaP.cnfpred: -------------------------------------------------------------------------------- 1 | 2 | T sse_real CHHHHHHHCCCCCEEEEEEEECCC-CEEEECCCCCCCHHHHHHHHHHC---CCEEEECCEEEEEEEEC----CCEEEEE 3 | T acc_real MMEMBBMEBMEEMBMBBBBBMMEB-EMMMMBEEBEBEBEMBBMBMEEE---MEMBEBEEMEBMMEMMM----EEMBBBM 4 | T 5zzaP 4 SLEQLAGRLISGDIGATAVIKMTG-EIIYQSPNWSVDGVHAINVYKNR---EPSIIIQGVKYSVIDVN----EDRLIAT 74 (121) 5 | **++||+++* .~+++|+||+**~ .*+***~~~~~~**~*++**+* -*+|+++**+||+|++* .**+|++ 6 | S ECU06_1350 18 VFDSLVGDLK-DDVLSLQLTNFDDVNHSYKSDGKCSMSVKDFDGYAE-NMPVKNVEYNGQKYIFMRSISDDAQPSQVFI 94 (147) 7 | S acc_pred MBEEBBEEBE-EMBBBBMBBMMEEMEMEMEEEMEMEEEMEMBEEMME-EBEMEMBMMEEMEBBBBMBBMEEMEMBBBBB 8 | S acc_conf 6776668686-964656574565545445757585446585745448-7664848547454677863558855365777 9 | S sse_pred HHHHHHHCCC-CCEEEEEEEECCCCCCCCCCCCCCCCCECCHHHHHC-CCCCCCEEECCEEEEEEEECCCCCCCEEEEE 10 | S sse_conf 8988875655-655887987578777655799965565445666654-6898866888989999985799998669999 11 | 12 | 13 | T sse_real EC------CCCEEEEEEEECCCEEEEEEECCCCCHHHHHHHHHHHHHHHHCCC 14 | T acc_real BE------EEEBMBBBBMBEEEBBBBBMBMEEBEBEEBBEMBMEBBEMBMEEM 15 | T 5zzaP 75 NV------GGQGHIVGAVAGGKALLIGYVSPNGDARTAYIQIDKTARQLSKIL 121 (121) 16 | |+ .****+||++*~*~*+++|++~ .~***+*++|+*++*++**** 17 | S ECU06_1350 95 SVDGDERGRKRGMLITSFCGILRMISTFDY--QIANSVTAKIFKVLGEYSCEE 145 (147) 18 | S acc_pred MBMEEEEEMEMBBBBBBBBEBBMBBBBBEM--EMBMMBBBMBBEBBEEMEMEE 19 | S acc_conf 444478855564678477646656764644--455547875987675664568 20 | S sse_pred EECCCCCCCCCEEEEHEHHHHEEEEEEECC--CCCCHHHHHHHHHHHCCCCCC 21 | S sse_conf 985898987544577656654357888656--566557899999865565655 22 | 23 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/CNFPRED/ECU06_1350-6iqkA.cnfpred: -------------------------------------------------------------------------------- 1 | 2 | T sse_real CCCCHHHHHHHHCCCCCCCC--CCCEEEEEECCC-CEEEECCCCCCCCHHHHHHHHHHHHCCCCHHHHCEEECCEEEEE 3 | T acc_real EEEEMMMBBEEEBBMEMEEM--EBEBBBBBBMEM-MMMBMBEEBMEBEEEBBEMBMMBBEEEEEBEEEBBMBMEMEBEM 4 | T 6iqkA 8 TNMSWQTYVDDHLMCDVAGN--RLTAAAILGQDG-SVWAQSNNFPQVKPEEIQGIKDDFTTPGTLAPTGLFLGGNKYMV 83 (140) 5 | ~****++++| .|++** -*****||+**~ -****~~~**~*~*~~+**+|** .~*~*|+++**+||+ 6 | S ECU06_1350 11 TNMEYADVFD-SLVGDL---KDDVLSLQLTNFDDVNHSYKSDGKCSMSVKDFDGYAEN------MPVKNVEYNGQKYIF 79 (147) 7 | S acc_pred EEMEMBEMBE-EBBEEB---EEMBBBBMBBMMEEMEMEMEEEMEMEEEMEMBEEMMEE------BEMEMBMMEEMEBBB 8 | S acc_conf 5766647677-666868---69646565745655454457575854465857454487------664848547454677 9 | S sse_pred CCHHHHHHHH-HHHHCC---CCCEEEEEEEECCCCCCCCCCCCCCCCCECCHHHHHCC------CCCCCEEECCEEEEE 10 | S sse_conf 8754789898-887565---56558879875787776557999655654456666546------898866888989999 11 | 12 | 13 | T sse_real EEEE----CCCEEEEEE------CCEEEEEEEC-CCEEEEEEECCCCCHHHHHHHHHHHHHHHHHH 14 | T acc_real MEME----EEMBBMBME------EEBBBBBBMB-EMBBBBBBBMEEBEEEMBMEBBMEBBEMBMEM 15 | T 6iqkA 84 IQGE----PNAVIRGKK------GAGGVTIKKT-TQALVFGIYDEPMTPGQCNLVVENLGEYLIES 138 (140) 16 | |+** .~**|||++ -**+++||+* -***+|+|++*~~~~***++++++|+**+~** 17 | S ECU06_1350 80 MRSISDDAQPSQVFISVDGDERGRKRGMLITSFCGILRMISTFDYQIANSVTAKIFKVLGEYSCEE 145 (147) 18 | S acc_pred BMBBMEEMEMBBBBBMBMEEEEEMEMBBBBBBBBEBBMBBBBBEMEMBMMBBBMBBEBBEEMEMEE 19 | S acc_conf 863558855365777444478855564678477646656764644455547875987675664568 20 | S sse_pred EEECCCCCCCEEEEEEECCCCCCCCCEEEEHEHHHHEEEEEEECCCCCCHHHHHHHHHHHCCCCCC 21 | S sse_conf 985799998669999985898987544577656654357888656566557899999865565655 22 | 23 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/CNFPRED/ECU08_1425-1l1oA.cnfpred: -------------------------------------------------------------------------------- 1 | 2 | T sse_real EEEEEEEEEEECCCCCEEEEECCCCCEEEEEECCCCCCCCCCEEEEEEEECCCCCEEEEEEEECCCCCC-CCCHHHHHH 3 | T acc_real MBBBBBMMEEEMEEMMMBMBBBMEEEEBMBMMEEEMEEEBEMBBMBMBMBMEEMBBMMEEMEMMEMEEE-EMEBEEMBE 4 | T 1l1oA 24 PVCFVGRLEKIHPTGKMFILSDGEGKNGTIELMEPLDEEISGIVEVVGRVTAKATILCTSYVQFKEDSH-PFDLGLYNE 101 (121) 5 | *+|++||*+***~ .~*+||++*~ .*+|||+**~* .***+||||+|++* .*+|+***+** -*++**++* 6 | S ECU08_1425 13 TVYSFGKVRDKLE-NGKYEVSFRE-KTIIITTDRRL--SIGSWIRMYGTFKS-GVLRTIFVGEL-----DGVDINLLEK 81 (92) 7 | S acc_pred MBMBBBEBMMMBE-EMEBMBMMME-EMBBBMBEEEB--EEEMBBMBBBMBEE-EBBMBMBBBEB-----EEBMBMBBBM 8 | S acc_conf 5855765654557-8454575555-54648455666--45767959675755-45657577445-----5485758846 9 | S sse_pred EEEEECCEEEEEC-CCEEEEEEEE-EEEEEEECCEE--CCCCEEEEEEEEEC-CEEEEEEEEEE-----CCEHHHHHHH 10 | S sse_conf 8999654788765-9689999964-58999978766--77878999989876-87999999665-----5533898999 11 | 12 | 13 | T sse_real HHHHHHHCCCC 14 | T acc_real EBMEBMEMEEE 15 | T 1l1oA 102 AVKIIHDFPQF 112 (121) 16 | +++*|+*+*~* 17 | S ECU08_1425 82 AVRYVACRRKI 92 (92) 18 | S acc_pred BBMBBMMEEEE 19 | S acc_conf 97567556897 20 | S sse_pred HHHHHHHHHCC 21 | S sse_conf 99998876469 22 | 23 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/CNFPRED/ECU08_1425-2pi2E.cnfpred: -------------------------------------------------------------------------------- 1 | 2 | T sse_real EEEEEEEEEEECCCCCEEEEECCCCCEEEEECCCCCCCCCCCEEEEEEEECCCCCEEEEEEEECCCCCC-CCCHHHHHH 3 | T acc_real MBBBBBMMEEMMEEMMMBBBBBMEEEEBMBMMEEEMEEEBEMBBMBBBMBMEEMMBMBEMMEMMEMEEE-EMEBEEMBE 4 | T 2pi2E 45 PVCFVGRLEKIHPTGKMFILSDGEGKNGTIELMEPLDEEISGIVEVVGRVTAKATILCTSYVQFKEDSH-PFDLGLYNE 122 (142) 5 | *+|+++|+++**~ .~*+||++*~ .*+|+|+~~~* .*~*+|||||||+* .*+|+++*+** -*++*++** 6 | S ECU08_1425 13 TVYSFGKVRDKLE-NGKYEVSFRE-KTIIITTDRRL--SIGSWIRMYGTFKS-GVLRTIFVGEL-----DGVDINLLEK 81 (92) 7 | S acc_pred MBMBBBEBMMMBE-EMEBMBMMME-EMBBBMBEEEB--EEEMBBMBBBMBEE-EBBMBMBBBEB-----EEBMBMBBBM 8 | S acc_conf 5855765654557-8454575555-54648455666--45767959675755-45657577445-----5485758846 9 | S sse_pred EEEEECCEEEEEC-CCEEEEEEEE-EEEEEEECCEE--CCCCEEEEEEEEEC-CEEEEEEEEEE-----CCEHHHHHHH 10 | S sse_conf 8999654788765-9689999964-58999978766--77878999989876-87999999665-----5533898999 11 | 12 | 13 | T sse_real HHHHHHHCCCC 14 | T acc_real MBMEMMEEEEE 15 | T 2pi2E 123 AVKIIHDFPQF 133 (142) 16 | +|+*+****~* 17 | S ECU08_1425 82 AVRYVACRRKI 92 (92) 18 | S acc_pred BBMBBMMEEEE 19 | S acc_conf 97567556897 20 | S sse_pred HHHHHHHHHCC 21 | S sse_conf 99998876469 22 | 23 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/CNFPRED/ECU08_1425-3kf6B.cnfpred: -------------------------------------------------------------------------------- 1 | 2 | T sse_real EEEEEEEEEEEE-CCEEEEEECCEEEEEECCCCCCCC-CCCCCCEEEEEEEEEECCEEEEEEEEECCCCCHHHHHHHHH 3 | T acc_real BBEBBBBBMMME-EMMBMBMMEEMMBMBMBEEMEMEE-EMEEEMMBMBMBMBMEEMBBMBMMMEEBEEMEMEEMEEEBM 4 | T 3kf6B 23 KLRFLGCVQSYK-NGILRLIDGSSSVTCDVTVVLPDV-SIQKHEWLNIVGRKRQDGIVDVLLIRSAVGINLPRYRQMVS 99 (105) 5 | +++*+++*|+** .~*+|||*+*~*+|+|+* -+***++||||||+|+ .*+|++++***~~+*+***+**++ 6 | S ECU08_1425 13 TVYSFGKVRDKLENGKYEVSFREKTIIITTD------RRLSIGSWIRMYGTFKS-GVLRTIFVGELDGVDINLLEKAVR 84 (92) 7 | S acc_pred MBMBBBEBMMMBEEMEBMBMMMEEMBBBMBE------EEBEEEMBBMBBBMBEE-EBBMBMBBBEBEEBMBMBBBMBBM 8 | S acc_conf 5855765654557845457555554648455------66645767959675755-456575774455485758846975 9 | S sse_pred EEEEECCEEEEECCCEEEEEEEEEEEEEEEC------CEECCCCEEEEEEEEEC-CEEEEEEEEEECCEHHHHHHHHHH 10 | S sse_conf 8999654788765968999996458999978------76677878999989876-879999996655533898999999 11 | 12 | 13 | T sse_real HHHHCC 14 | T acc_real EEEEEE 15 | T 3kf6B 100 ERQKCD 105 (105) 16 | ****** 17 | S ECU08_1425 85 YVACRR 90 (92) 18 | S acc_pred BBMMEE 19 | S acc_conf 675568 20 | S sse_pred HHHHHH 21 | S sse_conf 988764 22 | 23 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/CNFPRED/ECU08_1425-4gnxA.cnfpred: -------------------------------------------------------------------------------- 1 | 2 | T sse_real EEEEEEEEEEEE-CCEEEEEECCCCEEEEECCCCCCCCCCCEEEEEEEEECCCCEEEEEEEEECCCC----CCCHHHHH 3 | T acc_real MBMBBBEMEEME-EEMBMBMBMMEMMBEBEMMEEMEBEEBMMBMBMBEBMEEEEMBEBEEMEMMMEE----EMEMEEMM 4 | T 4gnxA 20 TVRIVGKVHKVT-GNTLLMQTSDLGNVEIAMTPDSDVSSSTFVEVTGKVSDAGSSFQANQIREFTTVDCGHDVDLTLVE 97 (114) 5 | *+|++|+*++** .**+||++** .*+++|*~ .~**~***||||+|++* .*++++*++**~ -*++***+ 6 | S ECU08_1425 13 TVYSFGKVRDKLENGKYEVSFRE-KTIIITTD--RRLSIGSWIRMYGTFKS--GVLRTIFVGELD------GVDINLLE 80 (92) 7 | S acc_pred MBMBBBEBMMMBEEMEBMBMMME-EMBBBMBE--EEBEEEMBBMBBBMBEE--EBBMBMBBBEBE------EBMBMBBB 8 | S acc_conf 58557656545578454575555-54648455--66645767959675755--456575774455------48575884 9 | S sse_pred EEEEECCEEEEECCCEEEEEEEE-EEEEEEEC--CEECCCCEEEEEEEEEC--CEEEEEEEEEEC------CEHHHHHH 10 | S sse_conf 89996547887659689999964-58999978--76677878999989876--879999996655------53389899 11 | 12 | 13 | T sse_real HHHHHHHCCHHH 14 | T acc_real EMBEEMEEEEEE 15 | T 4gnxA 98 NVVQISAAFPNL 109 (114) 16 | *+|+*+****** 17 | S ECU08_1425 81 KAVRYVACRRKI 92 (92) 18 | S acc_pred MBBMBBMMEEEE 19 | S acc_conf 697567556897 20 | S sse_pred HHHHHHHHHHCC 21 | S sse_conf 999998876469 22 | 23 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/CNFPRED/ECU08_1425-4joiC.cnfpred: -------------------------------------------------------------------------------- 1 | 2 | T sse_real CCEEEEEEEEEEEECC-CCEEEEEEECCCCEEEEEEECCCCCCC-CCCCCCEEEEEEEEECCCCCCCEEEEEEEEECCC 3 | T acc_real EMMBMBBBMBMEMEEE-EMMBMBMBEEEEEEMEBMBMBEEMMEM-EEEEEBBBMBMBMBMEMEEEEMBBEBMEMEMMEE 4 | T 4joiC 22 GSTLRTFGRLCLYDMI-QSRVTLMAQHGSDQHQVLVCTKLVEPF-HAQVGSLYIVLGELQHQQDRGSVVKARVLTCVEG 98 (122) 5 | ~*+||+|||+++** .*++|||++ -**+||||* -*~~*++||||+||+* .*|+++**+**** 6 | S ECU08_1425 11 GRTVYSFGKVRDKL--ENGKYEVSFR----EKTIIITTD-----RRLSIGSWIRMYGTFKS-----GVLRTIFVGELDG 73 (92) 7 | S acc_pred EEMBMBBBEBMMMB--EEMEBMBMMM----EEMBBBMBE-----EEBEEEMBBMBBBMBEE-----EBBMBMBBBEBEE 8 | S acc_conf 55585576565455--7845457555----554648455-----66645767959675755-----4565757744554 9 | S sse_pred CCEEEEECCEEEEE--CCCEEEEEEE----EEEEEEEEC-----CEECCCCEEEEEEEEEC-----CEEEEEEEEEECC 10 | S sse_conf 96899965478876--5968999996----458999978-----76677878999989876-----8799999966555 11 | 12 | 13 | T sse_real CCHHHHHHHHHHHHHHHHH 14 | T acc_real MEBEEMMMEBEEEMMEEEE 15 | T 4joiC 99 MNLPLLEQAIREQRLYKQE 117 (122) 16 | +++++||*+++******** 17 | S ECU08_1425 74 VDINLLEKAVRYVACRRKI 92 (92) 18 | S acc_pred BMBMBBBMBBMBBMMEEEE 19 | S acc_conf 8575884697567556897 20 | S sse_pred EHHHHHHHHHHHHHHHHCC 21 | S sse_conf 3389899999998876469 22 | 23 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/FASTA_ALN/ECU03_1140-2pi2A.fasta: -------------------------------------------------------------------------------- 1 | >2pi2A 2 | MWNSGFESYGSSSYGGAGGYTQSPGGFGSPAPSQAEKKSRARAQHI--------VPCTISQLLSATLVDEVFRIGNVEISQVTIVGIIRHAEKAPT-NIVYKIDDMTAAPMDVRQWVDTDDTSSEN-TVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSKANSQPSAGRAPISNPGMSEAGNFGGNSFMPANGLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIYSTVDDDHFKSTDAE 3 | 4 | 5 | >ECU03_1140 6 | ----------------------------------------------MTSRVGPPLRILSDSLKKLRRVSGAIFYGRREVSHVEIAGTCIDR-----GRVFARILDF-CGEVLVEIG----------DQKIALGSSYLLVCKVQARSGGIGLHCKSAKRLGIFEEMF-FWAEAVNLEGGLQ---------------------------------------------------------------------------------------------------- 7 | 8 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/FASTA_ALN/ECU03_1140-3kdfB.fasta: -------------------------------------------------------------------------------- 1 | >3kdfB 2 | SRAQH-------IVPCTISQLLSATLVDEVFRIGNVEISQVTIVGIIRHAEKAPT-NIVYKIDDMTAAPMDVRQWVDTDDTSSEN-TVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSKA 3 | 4 | 5 | >ECU03_1140 6 | -----MTSRVGPPLRILSDSLKKLRRVSGAIFYGRREVSHVEIAGTCIDR-----GRVFARILDF-CGEVLVEIG----------DQKIALGSSYLLVCKVQARSGGIGLHCKSAKRLGI-FEEMFFWAEAVNLEGGLQ-- 7 | 8 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/FASTA_ALN/ECU03_1140-3kf6A.fasta: -------------------------------------------------------------------------------- 1 | >3kf6A 2 | SLENENQLTHQFPTLSRW--------NPMFISDVHKISFHPHLQR-YIGFWMGFPIRWIQIVGYIAAIDIYEGKHVLTVDDCSGMVLRVVFIIQDDFSMSKRAISMSPGNVVCVFGKINSFRSEVELIAQSFEELRDPNDEWKAWQKRMRYKKNLTKISKNHHSIIRT 3 | 4 | 5 | >ECU03_1140 6 | ------------------MTSRVGPPLRILSDSLKKLRRV-----SGAIFYGRREVSHVEIAGTCIDR----GRVFARILDF---CGEVLVEIGD--------QKIALGSSYLLVCKVQARSGGIGLHCKSAKRLG-IFEEMFFWAEAVNLEGGLQ------------ 7 | 8 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/FASTA_ALN/ECU03_1140-4gnxB.fasta: -------------------------------------------------------------------------------- 1 | >4gnxB 2 | GKKAGNNTLRPVTIRQILNAEQPHPDA------------------------EFILDGAELGQLTFVAVVRNISRNAT-NVAYSVEDGTGQIEVRQWLDSSSDDSSKA-SEIRNNVYVRVLGTLKSFQNRRSISSGHMRPVIDYNEVMFHRLEAVHAHLQVTR 3 | 4 | 5 | >ECU03_1140 6 | ---------------------------MTSRVGPPLRILSDSLKKLRRVSGAIFYGRREVSHVEIAGTCIDR-----GRVFARILDFCGEVLVEIG-----------DQKIALGSSYLLVCKVQARSGGIGLHCKSAKRLG-IFEEMFFWAEAVNLEGGLQ- 7 | 8 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/FASTA_ALN/ECU03_1140-4joiA.fasta: -------------------------------------------------------------------------------- 1 | >4joiA 2 | LDPVFLAF--------AKLYIRDILDMKESRQVPGVFLYNGHPIKQVDVLGTVIGVRERDA-FYSYGVDDSTGVINCICWKKLNTESVSAAPSAARELSLTSQLKKLQETIEQK-TKIEIGDTIRVRGSIRTYREEREIHATTYYKVDDPVWNIQIARMLELPTIYRKVYDQPFHS 3 | 4 | 5 | >ECU03_1140 6 | --------MTSRVGPPLRILSDSLKKLRRV---SGAIFYGRREVSHVEIAGTCIDR-----GRVFARILDFCGEVLVEIG----------------------------------DQKIALGSSYLLVCKVQARSGGIGLHCKSAKRLGI---FEEMFFWAEAVNLEGGLQ------ 7 | 8 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/FASTA_ALN/ECU06_1350-2vk3A.fasta: -------------------------------------------------------------------------------- 1 | >2vk3A 2 | GS-----------MAGWQSYVDNLMCDG--CCQEAAIVGYCDAK-YVWAATAGGVFQSITPAEIDVIIGKDREG-FFTNGLTLGGKKCSVIRDSLYVDSDCTMDIRTKSQGGEPTYNVAVGRAGRVLVFVMGKEGVHGGGLNKKAYSMAKYLRDSGF- 3 | 4 | 5 | >ECU06_1350 6 | --MPGIIYEGKGTNMEYADVFDSLVGDLKDDVLSLQLTNFDD--VNHSYKS--DGKCSMSVKDFDGYAE-----NMPVKNVEYNGQKYIFMRSISDDAQPSQVFISVDGDERGRKRGMLITSFCGILRMISTFDYQIANSVTAKIFKVLGEYSCEEEE 7 | 8 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/FASTA_ALN/ECU06_1350-3h20A.fasta: -------------------------------------------------------------------------------- 1 | >3h20A 2 | MKNDRT---------------LQAIGRQLKAMGCERFDIGVRDATTGQMMNR-----EWSAAEVLQNTPWLKRMNA----QGNDVYIRPAE-QERHGLVLVDDLSEFDLDDMKAE-GREPALVVETSPKNYQAWVKVADAAGGELRGQIARTLASEYDADPASADSRHYGRLAGFTNRKDKHTTRAGYQPWVLLRESKGKTATAGPALVQQAGQQIEQAQRQQEKARRLASLELPERQLSRHRRTALDEYRSEMAGLVKRFGDDLSKCDFIAAQKLASRGRSAEEIGKAMAEASPALAERKPGHEADYIERTVSKVMGLPSVQLARAELARAPAPRQRGMDRGGPDFSM 3 | 4 | 5 | >ECU06_1350 6 | ------MPGIIYEGKGTNMEYADVFDSLVGDLKDDVLSLQLTNFDDVNHSYKSDGKCSMSVKDFDGYAENMPVKN-VEYNGQKYIFMRSISDDAQPSQVFISVDGDE--------RGRKRGMLITSFCGILRMISTFDYQIANSVTAKIFKVLGEYSCEEEE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 7 | 8 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/FASTA_ALN/ECU06_1350-4qwoA.fasta: -------------------------------------------------------------------------------- 1 | >4qwoA 2 | MHHHHHHSSGVDLGTENLYFQSNAM------------AEWHKIIEDISKN--NKFEDAAIVDYKTTKNVLAAIPNR-TFAKINPGEVIPLITNHNILKPLIGQKFCIVYTNSLMDENTYAMELLTGY---APVSPIVIARTHTALIFLMGKPTTSRRDVYRTCRDHATRVRATGN- 3 | 4 | 5 | >ECU06_1350 6 | -------------------------MPGIIYEGKGTNMEYADVFDSLVGDLKDDVLSLQLTNFDDVNHSYKS----DGKCSMSVKDFDGYAENMPVKNVEYNGQKYIFMRSISDDAQPSQVFISVDGDERGRKRGMLITSFCGILRMISTFDYQIANSVTAKIFKVLGEYSCEEEE 7 | 8 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/FASTA_ALN/ECU06_1350-5zzaP.fasta: -------------------------------------------------------------------------------- 1 | >5zzaP 2 | GPM-----------------SLEQLAGRLISGDIGATAVIKMTG-EIIYQSPNWSVDGVHAINVYKNR---EPSIIIQGVKYSVIDVN----EDRLIATNV------GGQGHIVGAVAGGKALLIGYVSPNGDARTAYIQIDKTARQLSKIL-- 3 | 4 | 5 | >ECU06_1350 6 | ---MPGIIYEGKGTNMEYADVFDSLVGDLK-DDVLSLQLTNFDDVNHSYKSDGKCSMSVKDFDGYAE-NMPVKNVEYNGQKYIFMRSISDDAQPSQVFISVDGDERGRKRGMLITSFCGILRMISTFDY--QIANSVTAKIFKVLGEYSCEEEE 7 | 8 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/FASTA_ALN/ECU06_1350-6iqkA.fasta: -------------------------------------------------------------------------------- 1 | >6iqkA 2 | KVKKAAA----------TNMSWQTYVDDHLMCDVAGN--RLTAAAILGQDG-SVWAQSNNFPQVKPEEIQGIKDDFTTPGTLAPTGLFLGGNKYMVIQGE----PNAVIRGKK------GAGGVTIKKT-TQALVFGIYDEPMTPGQCNLVVENLGEYLIESGL-- 3 | 4 | 5 | >ECU06_1350 6 | -------MPGIIYEGKGTNMEYADVFD-SLVGDL---KDDVLSLQLTNFDDVNHSYKSDGKCSMSVKDFDGYAEN------MPVKNVEYNGQKYIFMRSISDDAQPSQVFISVDGDERGRKRGMLITSFCGILRMISTFDYQIANSVTAKIFKVLGEYSCEE--EE 7 | 8 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/FASTA_ALN/ECU08_1425-1l1oA.fasta: -------------------------------------------------------------------------------- 1 | >1l1oA 2 | MVDMMDLPRSRINAGMLAQFIDK------------PVCFVGRLEKIHPTGKMFILSDGEGKNGTIELMEPLDEEISGIVEVVGRVTAKATILCTSYVQFKEDSH-PFDLGLYNEAVKIIHDFPQFYPLGIVQHD 3 | 4 | 5 | >ECU08_1425 6 | -----------------------MLRLLDIPVEGRTVYSFGKVRDKLE-NGKYEVSFRE-KTIIITTDRRL--SIGSWIRMYGTFKS-GVLRTIFVGEL-----DGVDINLLEKAVRYVACRRKI--------- 7 | 8 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/FASTA_ALN/ECU08_1425-2pi2E.fasta: -------------------------------------------------------------------------------- 1 | >2pi2E 2 | MGHHHHHHHHHHSSGHIEGRHMVDMMDLPRSRINAGMLAQFIDK------------PVCFVGRLEKIHPTGKMFILSDGEGKNGTIELMEPLDEEISGIVEVVGRVTAKATILCTSYVQFKEDSH-PFDLGLYNEAVKIIHDFPQFYPLGIVQHD 3 | 4 | 5 | >ECU08_1425 6 | --------------------------------------------MLRLLDIPVEGRTVYSFGKVRDKLE-NGKYEVSFRE-KTIIITTDRRL--SIGSWIRMYGTFKS-GVLRTIFVGEL-----DGVDINLLEKAVRYVACRRKI--------- 7 | 8 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/FASTA_ALN/ECU08_1425-3kf6B.fasta: -------------------------------------------------------------------------------- 1 | >3kf6B 2 | PLGSDSAKLIFINQINDCKDGQ------------KLRFLGCVQSYK-NGILRLIDGSSSVTCDVTVVLPDV-SIQKHEWLNIVGRKRQDGIVDVLLIRSAVGINLPRYRQMVSERQKCD-- 3 | 4 | 5 | >ECU08_1425 6 | ----------------------MLRLLDIPVEGRTVYSFGKVRDKLENGKYEVSFREKTIIITTD------RRLSIGSWIRMYGTFKS-GVLRTIFVGELDGVDINLLEKAVRYVACRRKI 7 | 8 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/FASTA_ALN/ECU08_1425-4gnxA.fasta: -------------------------------------------------------------------------------- 1 | >4gnxA 2 | MEKPTPLINSSMLGQYVGQ------------TVRIVGKVHKVT-GNTLLMQTSDLGNVEIAMTPDSDVSSSTFVEVTGKVSDAGSSFQANQIREFTTVDCGHDVDLTLVENVVQISAAFPNLFSDST 3 | 4 | 5 | >ECU08_1425 6 | -------------------MLRLLDIPVEGRTVYSFGKVRDKLENGKYEVSFRE-KTIIITTD--RRLSIGSWIRMYGTFKS--GVLRTIFVGELD------GVDINLLEKAVRYVACRRKI----- 7 | 8 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/FASTA_ALN/ECU08_1425-4joiC.fasta: -------------------------------------------------------------------------------- 1 | >4joiC 2 | MLPKPGTYYLPWEVSAGQVPD----------GSTLRTFGRLCLYDMI-QSRVTLMAQHGSDQHQVLVCTKLVEPF-HAQVGSLYIVLGELQHQQDRGSVVKARVLTCVEGMNLPLLEQAIREQRLYKQERGGSQ 3 | 4 | 5 | >ECU08_1425 6 | ---------------------MLRLLDIPVEGRTVYSFGKVRDKL--ENGKYEVSFR----EKTIIITTD-----RRLSIGSWIRMYGTFKS-----GVLRTIFVGELDGVDINLLEKAVRYVACRRKI----- 7 | 8 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Folding/RAPTORX_3D/raptorx.log: -------------------------------------------------------------------------------- 1 | COMMAND LINE: 2 | raptorx.pl -t 20 -k 5 -i RESULTS_20210915//FASTA -o RESULTS_20210915//Folding/RAPTORX_3D/ 3 | raptorx.pl version = 0.6e 4 | Using MODELLER binary version mod10.1 5 | 3D Folding started on: Wed Sep 15 14:43:30 2021 6 | Time to fold ECU03_1140.fasta = 24.07 minutes 7 | Time to fold ECU03_1140.fasta = 24.07 minutes (cumulative) 8 | Time to fold ECU06_1350.fasta = 22.28 minutes 9 | Time to fold ECU06_1350.fasta = 46.35 minutes (cumulative) 10 | Time to fold ECU08_1425.fasta = 15.10 minutes 11 | Time to fold ECU08_1425.fasta = 61.45 minutes (cumulative) 12 | 3D Folding ended on Wed Sep 15 15:44:57 2021 13 | 14 | OUTPUT directory = /home/jpombert/TEST/RESULTS_20210915/Folding/RAPTORX_3D 15 | PDB/: Contains the protein structure(s) (.pdb) predicted for each FASTA files 16 | TGT/: Contains the feature files (.tgt) generated for each FASTA files 17 | RANK/: Contains the lists (.rank) of the best templates/models found for each FASTA files 18 | FASTA_ALN/: Contains pairwise alignments between FASTA sequences and their best template(s)/model(s) found in FASTA format 19 | CNFPRED/: Contains pairwise alignments between FASTA sequences and their best template(s)/model(s) found in CNFPRED format 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Sorted by q-scores: duplicated RCSB PDB entries are not shown 3 | ECU03_1140-m2 ALPHAFOLD 3KDF D 0.6744 1.6116 0.1545 110 119 pdb3kdf.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 4 | ECU03_1140-m5 ALPHAFOLD 1QUQ C 0.6615 1.6806 0.1545 110 119 pdb1quq.ent.gz PROTEIN (REPLICATION PROTEIN A 32 KD SUBUNIT) 5 | ECU03_1140-m2 ALPHAFOLD 2PQA A 0.6578 1.6328 0.1593 113 128 pdb2pqa.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 6 | ECU03_1140-m5 ALPHAFOLD 3KDF B 0.6562 1.7378 0.1545 110 118 pdb3kdf.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 7 | ECU03_1140-m5 ALPHAFOLD 4GNX B 0.6529 1.6388 0.1182 110 122 pdb4gnx.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 8 | ECU03_1140-m2 ALPHAFOLD 4GOP B 0.6513 1.6472 0.1182 110 122 pdb4gop.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 9 | 10 | ### ECU06_1350; Top matches across all predictors. Sorted by q-scores: duplicated RCSB PDB entries are not shown 11 | ECU06_1350-m1 ALPHAFOLD 3D9Y B 0.4406 1.9654 0.1296 108 126 pdb3d9y.ent.gz PROFILIN 12 | ECU06_1350-m1 ALPHAFOLD 3DAV B 0.4366 1.9341 0.1308 107 126 pdb3dav.ent.gz PROFILIN 13 | ECU06_1350-m3 ALPHAFOLD 4QWO B 0.4335 2.2693 0.0435 115 132 pdb4qwo.ent.gz PROFILIN 14 | ECU06_1350-m2 ALPHAFOLD 5YED A 0.4327 2.4289 0.0940 117 130 pdb5yed.ent.gz UNCHARACTERIZED PROTEIN 15 | ECU06_1350-m2 ALPHAFOLD 5YEE A 0.4324 2.4702 0.0833 120 135 pdb5yee.ent.gz UNCHARACTERIZED PROTEIN 16 | ECU06_1350-m2 ALPHAFOLD 3D9Y A 0.4324 2.0264 0.1296 108 126 pdb3d9y.ent.gz PROFILIN 17 | ECU06_1350-m1 ALPHAFOLD 1YPR A 0.4294 2.1337 0.1193 109 125 pdb1ypr.ent.gz PROFILIN 18 | ECU06_1350-m3 ALPHAFOLD 5ZZA P 0.4264 2.0743 0.1143 105 119 pdb5zza.ent.gz UNCHARACTERIZED PROTEIN 19 | ECU06_1350-m3 ALPHAFOLD 3DAV A 0.4252 2.1972 0.1091 110 126 pdb3dav.ent.gz PROFILIN 20 | 21 | ### ECU08_1425; Top matches across all predictors. Sorted by q-scores: duplicated RCSB PDB entries are not shown 22 | ECU08_1425-m4 ALPHAFOLD 3K0X A 0.6395 1.6419 0.1149 87 99 pdb3k0x.ent.gz PROTEIN TEN1 23 | ECU08_1425-m4 ALPHAFOLD 3KF6 B 0.6274 1.5809 0.1250 88 105 pdb3kf6.ent.gz PROTEIN TEN1 24 | ECU08_1425-m1 ALPHAFOLD 5DOI F 0.6070 1.7966 0.1310 84 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 25 | ECU08_1425-m1 ALPHAFOLD 5DOI H 0.5996 1.8383 0.1310 84 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 26 | ECU08_1425-m4 ALPHAFOLD 5DOI G 0.5986 1.8436 0.1310 84 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 27 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Homology/GESAMT/All_GESAMT_matches_per_protein.tsv: -------------------------------------------------------------------------------- 1 | 2 | ### ECU03_1140; Top matches across all predictors. Sorted by q-scores: duplicated RCSB PDB entries are not shown 3 | ECU03_1140-m4 RAPTORX 3KDF B 0.8223 0.6475 0.1560 109 118 pdb3kdf.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 4 | ECU03_1140-m4 RAPTORX 1QUQ A 0.7851 0.7877 0.1560 109 121 pdb1quq.ent.gz PROTEIN (REPLICATION PROTEIN A 32 KD SUBUNIT) 5 | ECU03_1140-m4 RAPTORX 3KDF D 0.7850 0.9820 0.1545 110 119 pdb3kdf.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 6 | ECU03_1140-m4 RAPTORX 1L1O E 0.7839 0.8083 0.1545 110 123 pdb1l1o.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 7 | ECU03_1140-m4 RAPTORX 2PI2 D 0.7821 0.7078 0.1560 109 123 pdb2pi2.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 8 | ECU03_1140-m3 RAPTORX 1L1O B 0.7550 1.0115 0.1545 110 123 pdb1l1o.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 9 | ECU03_1140-m3 RAPTORX 2PI2 B 0.7530 0.8878 0.1560 109 124 pdb2pi2.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 10 | ECU03_1140-m1 RAPTORX 1QUQ C 0.6763 1.3940 0.1589 107 119 pdb1quq.ent.gz PROTEIN (REPLICATION PROTEIN A 32 KD SUBUNIT) 11 | ECU03_1140-m1 RAPTORX 3KF6 A 0.6704 1.0992 0.1364 110 136 pdb3kf6.ent.gz PROTEIN STN1 12 | ECU03_1140-m2 ALPHAFOLD 2PQA A 0.6578 1.6328 0.1593 113 128 pdb2pqa.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 13 | ECU03_1140-m1 RAPTORX 4GNX B 0.6551 1.4212 0.1215 107 122 pdb4gnx.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 14 | ECU03_1140-m2 ALPHAFOLD 4GOP B 0.6513 1.6472 0.1182 110 122 pdb4gop.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 15 | ECU03_1140-m2 RAPTORX 4JOI A 0.6316 0.9430 0.1215 107 141 pdb4joi.ent.gz CST COMPLEX SUBUNIT STN1 16 | ECU03_1140-m5 RAPTORX 4GOP Y 0.5354 1.1860 0.1383 94 122 pdb4gop.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 17 | ECU03_1140-m5 RAPTORX 4GNX Y 0.5304 1.0308 0.1413 92 122 pdb4gnx.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 18 | 19 | ### ECU06_1350; Top matches across all predictors. Sorted by q-scores: duplicated RCSB PDB entries are not shown 20 | ECU06_1350-m3 RAPTORX 4QWO A 0.8062 0.6566 0.0543 129 134 pdb4qwo.ent.gz PROFILIN 21 | ECU06_1350-m3 RAPTORX 4QWO B 0.8006 0.7017 0.0547 128 132 pdb4qwo.ent.gz PROFILIN 22 | ECU06_1350-m1 RAPTORX 2VK3 A 0.7950 0.7701 0.0827 133 142 pdb2vk3.ent.gz PROFILIN-2 23 | ECU06_1350-m1 RAPTORX 2V8C A 0.7779 0.9305 0.0758 132 139 pdb2v8c.ent.gz PROFILIN-2 24 | ECU06_1350-m1 RAPTORX 1PNE A 0.7726 0.9662 0.0833 132 139 pdb1pne.ent.gz PROFILIN 25 | ECU06_1350-m1 RAPTORX 2V8F A 0.7715 0.9734 0.0833 132 139 pdb2v8f.ent.gz PROFILIN-2 26 | ECU06_1350-m1 RAPTORX 1HLU P 0.7687 0.9920 0.0833 132 139 pdb1hlu.ent.gz 27 | ECU06_1350-m3 RAPTORX 3UB5 P 0.7368 1.1222 0.0840 131 139 pdb3ub5.ent.gz PROFILIN-1 28 | ECU06_1350-m3 RAPTORX 1CF0 B 0.7337 1.1039 0.0846 130 138 pdb1cf0.ent.gz PROTEIN (PROFILIN) 29 | ECU06_1350-m3 RAPTORX 1CJF A 0.7333 1.1065 0.0846 130 138 pdb1cjf.ent.gz PROTEIN (HUMAN PLATELET PROFILIN) 30 | ECU06_1350-m2 RAPTORX 5ZZA P 0.7265 0.7277 0.1552 116 119 pdb5zza.ent.gz UNCHARACTERIZED PROTEIN 31 | ECU06_1350-m5 RAPTORX 6IQI B 0.7000 0.9682 0.1311 122 131 pdb6iqi.ent.gz PROFILIN-2 32 | ECU06_1350-m5 RAPTORX 6IQI A 0.6977 0.9394 0.1240 121 130 pdb6iqi.ent.gz PROFILIN-2 33 | ECU06_1350-m5 RAPTORX 6IQK C 0.6943 1.0286 0.1600 125 137 pdb6iqk.ent.gz PROFILIN-5 34 | ECU06_1350-m5 RAPTORX 6IQK G 0.6900 1.0579 0.1600 125 137 pdb6iqk.ent.gz PROFILIN-5 35 | ECU06_1350-m5 RAPTORX 1A0K A 0.6879 0.9268 0.1583 120 130 pdb1a0k.ent.gz PROFILIN 36 | ECU06_1350-m2 RAPTORX 5YED A 0.5297 1.6608 0.0957 115 130 pdb5yed.ent.gz UNCHARACTERIZED PROTEIN 37 | ECU06_1350-m2 RAPTORX 5ZZB A 0.5238 1.5926 0.0696 115 134 pdb5zzb.ent.gz UNCHARACTERIZED PROTEIN 38 | ECU06_1350-m2 RAPTORX 3D9Y B 0.5217 1.7006 0.1239 113 126 pdb3d9y.ent.gz PROFILIN 39 | ECU06_1350-m2 RAPTORX 3DAV B 0.5209 1.7059 0.1239 113 126 pdb3dav.ent.gz PROFILIN 40 | ECU06_1350-m4 RAPTORX 3H25 A 0.4862 0.9846 0.0574 122 188 pdb3h25.ent.gz REPLICATION PROTEIN B 41 | ECU06_1350-m1 ROSETTAFOLD 1YPR A 0.4623 2.0715 0.1250 112 125 pdb1ypr.ent.gz PROFILIN 42 | ECU06_1350-m1 ROSETTAFOLD 1YPR B 0.4515 2.0896 0.1351 111 125 pdb1ypr.ent.gz PROFILIN 43 | ECU06_1350-m2 ALPHAFOLD 5YEE A 0.4324 2.4702 0.0833 120 135 pdb5yee.ent.gz UNCHARACTERIZED PROTEIN 44 | ECU06_1350-m2 ALPHAFOLD 3D9Y A 0.4324 2.0264 0.1296 108 126 pdb3d9y.ent.gz PROFILIN 45 | ECU06_1350-m3 ALPHAFOLD 3DAV A 0.4252 2.1972 0.1091 110 126 pdb3dav.ent.gz PROFILIN 46 | ECU06_1350-m4 RAPTORX 6ZP9 B 0.3208 1.9261 0.0541 111 185 pdb6zp9.ent.gz PRIMPOL AEP DOMAIN (PP-N190) 47 | ECU06_1350-m4 RAPTORX 6ZP9 A 0.3159 2.0923 0.0531 113 185 pdb6zp9.ent.gz PRIMPOL AEP DOMAIN (PP-N190) 48 | 49 | ### ECU08_1425; Top matches across all predictors. Sorted by q-scores: duplicated RCSB PDB entries are not shown 50 | ECU08_1425-m4 ALPHAFOLD 3K0X A 0.6395 1.6419 0.1149 87 99 pdb3k0x.ent.gz PROTEIN TEN1 51 | ECU08_1425-m4 ALPHAFOLD 3KF6 B 0.6274 1.5809 0.1250 88 105 pdb3kf6.ent.gz PROTEIN TEN1 52 | ECU08_1425-m1 ALPHAFOLD 5DOI F 0.6070 1.7966 0.1310 84 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 53 | ECU08_1425-m1 ALPHAFOLD 5DOI H 0.5996 1.8383 0.1310 84 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 54 | ECU08_1425-m4 ALPHAFOLD 5DOI G 0.5986 1.8436 0.1310 84 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 55 | ECU08_1425-m1 ROSETTAFOLD 5DOI E 0.5768 1.8061 0.1098 82 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 56 | ECU08_1425-m1 RAPTORX 4JOI C 0.5518 1.1617 0.1807 83 118 pdb4joi.ent.gz CST COMPLEX SUBUNIT TEN1 57 | ECU08_1425-m1 RAPTORX 6W6W D 0.5463 1.4349 0.1765 85 117 pdb6w6w.ent.gz CST COMPLEX SUBUNIT TEN1 58 | ECU08_1425-m1 RAPTORX 4JOI D 0.5455 1.2119 0.1807 83 118 pdb4joi.ent.gz CST COMPLEX SUBUNIT TEN1 59 | ECU08_1425-m5 RAPTORX 4GOP X 0.5382 1.2259 0.1899 79 108 pdb4gop.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 60 | ECU08_1425-m5 RAPTORX 4GNX A 0.5375 1.2318 0.1899 79 108 pdb4gnx.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 61 | ECU08_1425-m5 RAPTORX 4GOP A 0.5348 1.2532 0.1899 79 108 pdb4gop.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 62 | ECU08_1425-m5 RAPTORX 4GNX X 0.5328 1.1591 0.1923 78 108 pdb4gnx.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 63 | ECU08_1425-m4 RAPTORX 1QUQ B 0.5170 1.2737 0.1750 80 114 pdb1quq.ent.gz PROTEIN (REPLICATION PROTEIN A 14 KD SUBUNIT) 64 | ECU08_1425-m4 RAPTORX 1L1O D 0.5165 1.2413 0.1625 80 115 pdb1l1o.ent.gz REPLICATION PROTEIN A 14 KDA SUBUNIT 65 | ECU08_1425-m4 RAPTORX 2PQA D 0.5149 1.2909 0.1625 80 114 pdb2pqa.ent.gz REPLICATION PROTEIN A 14 KDA SUBUNIT 66 | ECU08_1425-m4 RAPTORX 3KDF A 0.5126 1.2732 0.1750 80 115 pdb3kdf.ent.gz REPLICATION PROTEIN A 14 KDA SUBUNIT 67 | ECU08_1425-m4 RAPTORX 1L1O A 0.5118 1.2793 0.1625 80 115 pdb1l1o.ent.gz REPLICATION 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Sorted by q-scores: duplicated RCSB PDB entries are not shown 3 | ECU03_1140-m4 RAPTORX 3KDF B 0.8223 0.6475 0.1560 109 118 pdb3kdf.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 4 | ECU03_1140-m4 RAPTORX 1QUQ A 0.7851 0.7877 0.1560 109 121 pdb1quq.ent.gz PROTEIN (REPLICATION PROTEIN A 32 KD SUBUNIT) 5 | ECU03_1140-m4 RAPTORX 3KDF D 0.7850 0.9820 0.1545 110 119 pdb3kdf.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 6 | ECU03_1140-m4 RAPTORX 1L1O E 0.7839 0.8083 0.1545 110 123 pdb1l1o.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 7 | ECU03_1140-m4 RAPTORX 2PI2 D 0.7821 0.7078 0.1560 109 123 pdb2pi2.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 8 | ECU03_1140-m3 RAPTORX 1L1O B 0.7550 1.0115 0.1545 110 123 pdb1l1o.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 9 | ECU03_1140-m3 RAPTORX 2PI2 B 0.7530 0.8878 0.1560 109 124 pdb2pi2.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 10 | ECU03_1140-m1 RAPTORX 1QUQ C 0.6763 1.3940 0.1589 107 119 pdb1quq.ent.gz PROTEIN (REPLICATION PROTEIN A 32 KD SUBUNIT) 11 | ECU03_1140-m1 RAPTORX 3KF6 A 0.6704 1.0992 0.1364 110 136 pdb3kf6.ent.gz PROTEIN STN1 12 | ECU03_1140-m1 RAPTORX 4GNX B 0.6551 1.4212 0.1215 107 122 pdb4gnx.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 13 | ECU03_1140-m2 RAPTORX 4JOI A 0.6316 0.9430 0.1215 107 141 pdb4joi.ent.gz CST COMPLEX SUBUNIT STN1 14 | ECU03_1140-m5 RAPTORX 4GOP Y 0.5354 1.1860 0.1383 94 122 pdb4gop.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 15 | ECU03_1140-m5 RAPTORX 4GOP B 0.5345 1.1932 0.1383 94 122 pdb4gop.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 16 | ECU03_1140-m5 RAPTORX 4GNX Y 0.5304 1.0308 0.1413 92 122 pdb4gnx.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 17 | 18 | ### ECU06_1350; Top matches across all predictors. Sorted by q-scores: duplicated RCSB PDB entries are not shown 19 | ECU06_1350-m3 RAPTORX 4QWO A 0.8062 0.6566 0.0543 129 134 pdb4qwo.ent.gz PROFILIN 20 | ECU06_1350-m3 RAPTORX 4QWO B 0.8006 0.7017 0.0547 128 132 pdb4qwo.ent.gz PROFILIN 21 | ECU06_1350-m1 RAPTORX 2VK3 A 0.7950 0.7701 0.0827 133 142 pdb2vk3.ent.gz PROFILIN-2 22 | ECU06_1350-m1 RAPTORX 2V8C A 0.7779 0.9305 0.0758 132 139 pdb2v8c.ent.gz PROFILIN-2 23 | ECU06_1350-m1 RAPTORX 1PNE A 0.7726 0.9662 0.0833 132 139 pdb1pne.ent.gz PROFILIN 24 | ECU06_1350-m1 RAPTORX 2V8F A 0.7715 0.9734 0.0833 132 139 pdb2v8f.ent.gz PROFILIN-2 25 | ECU06_1350-m1 RAPTORX 1HLU P 0.7687 0.9920 0.0833 132 139 pdb1hlu.ent.gz 26 | ECU06_1350-m3 RAPTORX 3UB5 P 0.7368 1.1222 0.0840 131 139 pdb3ub5.ent.gz PROFILIN-1 27 | ECU06_1350-m3 RAPTORX 1CF0 B 0.7337 1.1039 0.0846 130 138 pdb1cf0.ent.gz PROTEIN (PROFILIN) 28 | ECU06_1350-m3 RAPTORX 1CJF A 0.7333 1.1065 0.0846 130 138 pdb1cjf.ent.gz PROTEIN (HUMAN PLATELET PROFILIN) 29 | ECU06_1350-m2 RAPTORX 5ZZA P 0.7265 0.7277 0.1552 116 119 pdb5zza.ent.gz UNCHARACTERIZED PROTEIN 30 | ECU06_1350-m5 RAPTORX 6IQI B 0.7000 0.9682 0.1311 122 131 pdb6iqi.ent.gz PROFILIN-2 31 | ECU06_1350-m5 RAPTORX 6IQI A 0.6977 0.9394 0.1240 121 130 pdb6iqi.ent.gz PROFILIN-2 32 | ECU06_1350-m5 RAPTORX 6IQK C 0.6943 1.0286 0.1600 125 137 pdb6iqk.ent.gz PROFILIN-5 33 | ECU06_1350-m5 RAPTORX 6IQK G 0.6900 1.0579 0.1600 125 137 pdb6iqk.ent.gz PROFILIN-5 34 | ECU06_1350-m5 RAPTORX 1A0K A 0.6879 0.9268 0.1583 120 130 pdb1a0k.ent.gz PROFILIN 35 | ECU06_1350-m2 RAPTORX 5YED A 0.5297 1.6608 0.0957 115 130 pdb5yed.ent.gz UNCHARACTERIZED PROTEIN 36 | ECU06_1350-m2 RAPTORX 5ZZB A 0.5238 1.5926 0.0696 115 134 pdb5zzb.ent.gz UNCHARACTERIZED PROTEIN 37 | ECU06_1350-m2 RAPTORX 3D9Y B 0.5217 1.7006 0.1239 113 126 pdb3d9y.ent.gz PROFILIN 38 | ECU06_1350-m2 RAPTORX 3DAV B 0.5209 1.7059 0.1239 113 126 pdb3dav.ent.gz PROFILIN 39 | ECU06_1350-m4 RAPTORX 3H25 A 0.4862 0.9846 0.0574 122 188 pdb3h25.ent.gz REPLICATION PROTEIN B 40 | ECU06_1350-m4 RAPTORX 6ZP9 B 0.3208 1.9261 0.0541 111 185 pdb6zp9.ent.gz PRIMPOL AEP DOMAIN (PP-N190) 41 | ECU06_1350-m4 RAPTORX 6ZP9 A 0.3159 2.0923 0.0531 113 185 pdb6zp9.ent.gz PRIMPOL AEP DOMAIN (PP-N190) 42 | 43 | ### ECU08_1425; Top matches across all predictors. Sorted by q-scores: duplicated RCSB PDB entries are not shown 44 | ECU08_1425-m1 RAPTORX 3K0X A 0.5866 1.3349 0.1125 80 99 pdb3k0x.ent.gz PROTEIN TEN1 45 | ECU08_1425-m1 RAPTORX 3KF6 B 0.5618 1.3716 0.1235 81 105 pdb3kf6.ent.gz PROTEIN TEN1 46 | ECU08_1425-m1 RAPTORX 4JOI C 0.5518 1.1617 0.1807 83 118 pdb4joi.ent.gz CST COMPLEX SUBUNIT TEN1 47 | ECU08_1425-m1 RAPTORX 6W6W D 0.5463 1.4349 0.1765 85 117 pdb6w6w.ent.gz CST COMPLEX SUBUNIT TEN1 48 | ECU08_1425-m1 RAPTORX 4JOI D 0.5455 1.2119 0.1807 83 118 pdb4joi.ent.gz CST COMPLEX SUBUNIT TEN1 49 | ECU08_1425-m5 RAPTORX 4GOP X 0.5382 1.2259 0.1899 79 108 pdb4gop.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 50 | ECU08_1425-m5 RAPTORX 4GNX A 0.5375 1.2318 0.1899 79 108 pdb4gnx.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 51 | ECU08_1425-m5 RAPTORX 4GOP A 0.5348 1.2532 0.1899 79 108 pdb4gop.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 52 | ECU08_1425-m5 RAPTORX 4GNX X 0.5328 1.1591 0.1923 78 108 pdb4gnx.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 53 | ECU08_1425-m4 RAPTORX 1QUQ B 0.5170 1.2737 0.1750 80 114 pdb1quq.ent.gz PROTEIN (REPLICATION PROTEIN A 14 KD SUBUNIT) 54 | ECU08_1425-m4 RAPTORX 1L1O D 0.5165 1.2413 0.1625 80 115 pdb1l1o.ent.gz REPLICATION PROTEIN A 14 KDA SUBUNIT 55 | ECU08_1425-m4 RAPTORX 2PQA D 0.5149 1.2909 0.1625 80 114 pdb2pqa.ent.gz REPLICATION PROTEIN A 14 KDA SUBUNIT 56 | ECU08_1425-m4 RAPTORX 3KDF A 0.5126 1.2732 0.1750 80 115 pdb3kdf.ent.gz REPLICATION PROTEIN A 14 KDA SUBUNIT 57 | ECU08_1425-m4 RAPTORX 1L1O A 0.5118 1.2793 0.1625 80 115 pdb1l1o.ent.gz REPLICATION PROTEIN A 14 KDA SUBUNIT 58 | ECU08_1425-m3 RAPTORX 2PQA B 0.4930 1.3648 0.1772 79 114 pdb2pqa.ent.gz REPLICATION PROTEIN A 14 KDA SUBUNIT 59 | ECU08_1425-m2 RAPTORX 5DOI G 0.4756 1.6689 0.1096 73 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 60 | ECU08_1425-m2 RAPTORX 5DOI E 0.4748 1.4721 0.1127 71 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 61 | ECU08_1425-m2 RAPTORX 5DOI F 0.4688 1.7198 0.1096 73 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 62 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Homology/GESAMT/ROSETTAFOLD/ECU03_1140-m1.normal.gesamt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PombertLab/3DFI/e4e0eb13e01393aa0cc4214b48860e80167a472e/Examples/Results_3DFI/Homology/GESAMT/ROSETTAFOLD/ECU03_1140-m1.normal.gesamt.gz -------------------------------------------------------------------------------- /Examples/Results_3DFI/Homology/GESAMT/ROSETTAFOLD/ECU06_1350-m1.normal.gesamt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PombertLab/3DFI/e4e0eb13e01393aa0cc4214b48860e80167a472e/Examples/Results_3DFI/Homology/GESAMT/ROSETTAFOLD/ECU06_1350-m1.normal.gesamt.gz -------------------------------------------------------------------------------- /Examples/Results_3DFI/Homology/GESAMT/ROSETTAFOLD/ECU08_1425-m1.normal.gesamt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PombertLab/3DFI/e4e0eb13e01393aa0cc4214b48860e80167a472e/Examples/Results_3DFI/Homology/GESAMT/ROSETTAFOLD/ECU08_1425-m1.normal.gesamt.gz -------------------------------------------------------------------------------- /Examples/Results_3DFI/Homology/GESAMT/ROSETTAFOLD_GESAMT_per_model.matches: -------------------------------------------------------------------------------- 1 | ### ECU03_1140-m1; Query mode = normal 2 | ECU03_1140-m1 1 3KDF D 0.5974 1.7114 0.1429 105 119 pdb3kdf.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 3 | ECU03_1140-m1 2 1QUQ C 0.5869 1.7728 0.1429 105 119 pdb1quq.ent.gz PROTEIN (REPLICATION PROTEIN A 32 KD SUBUNIT) 4 | ECU03_1140-m1 3 3KDF B 0.5791 1.5756 0.1386 101 118 pdb3kdf.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 5 | ECU03_1140-m1 4 4GNX B 0.5779 1.8052 0.1132 106 122 pdb4gnx.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 6 | ECU03_1140-m1 5 1QUQ A 0.5770 1.4966 0.1386 101 121 pdb1quq.ent.gz PROTEIN (REPLICATION PROTEIN A 32 KD SUBUNIT) 7 | ### ECU06_1350-m1; Query mode = normal 8 | ECU06_1350-m1 1 4QWO A 0.4758 2.3512 0.0407 123 134 pdb4qwo.ent.gz PROFILIN 9 | ECU06_1350-m1 2 4QWO B 0.4637 2.3247 0.0500 120 132 pdb4qwo.ent.gz PROFILIN 10 | ECU06_1350-m1 3 1YPR A 0.4623 2.0715 0.1250 112 125 pdb1ypr.ent.gz PROFILIN 11 | ECU06_1350-m1 4 1YPR B 0.4515 2.0896 0.1351 111 125 pdb1ypr.ent.gz PROFILIN 12 | ECU06_1350-m1 5 5ZZA P 0.4514 2.2460 0.1261 111 119 pdb5zza.ent.gz UNCHARACTERIZED PROTEIN 13 | ### ECU08_1425-m1; Query mode = normal 14 | ECU08_1425-m1 1 3K0X A 0.5951 1.8115 0.1163 86 99 pdb3k0x.ent.gz PROTEIN TEN1 15 | ECU08_1425-m1 2 5DOI H 0.5879 1.7411 0.1098 82 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 16 | ECU08_1425-m1 3 5DOI F 0.5875 1.7431 0.1098 82 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 17 | ECU08_1425-m1 4 5DOI G 0.5790 1.7088 0.1235 81 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 18 | ECU08_1425-m1 5 5DOI E 0.5768 1.8061 0.1098 82 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 19 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Homology/GESAMT/ROSETTAFOLD_GESAMT_per_protein.matches: -------------------------------------------------------------------------------- 1 | 2 | ### ECU03_1140; Top matches across all predictors. Sorted by q-scores: duplicated RCSB PDB entries are not shown 3 | ECU03_1140-m1 ROSETTAFOLD 3KDF D 0.5974 1.7114 0.1429 105 119 pdb3kdf.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 4 | ECU03_1140-m1 ROSETTAFOLD 1QUQ C 0.5869 1.7728 0.1429 105 119 pdb1quq.ent.gz PROTEIN (REPLICATION PROTEIN A 32 KD SUBUNIT) 5 | ECU03_1140-m1 ROSETTAFOLD 3KDF B 0.5791 1.5756 0.1386 101 118 pdb3kdf.ent.gz REPLICATION PROTEIN A 32 KDA SUBUNIT 6 | ECU03_1140-m1 ROSETTAFOLD 4GNX B 0.5779 1.8052 0.1132 106 122 pdb4gnx.ent.gz PUTATIVE UNCHARACTERIZED PROTEIN 7 | ECU03_1140-m1 ROSETTAFOLD 1QUQ A 0.5770 1.4966 0.1386 101 121 pdb1quq.ent.gz PROTEIN (REPLICATION PROTEIN A 32 KD SUBUNIT) 8 | 9 | ### ECU06_1350; Top matches across all predictors. Sorted by q-scores: duplicated RCSB PDB entries are not shown 10 | ECU06_1350-m1 ROSETTAFOLD 4QWO A 0.4758 2.3512 0.0407 123 134 pdb4qwo.ent.gz PROFILIN 11 | ECU06_1350-m1 ROSETTAFOLD 4QWO B 0.4637 2.3247 0.0500 120 132 pdb4qwo.ent.gz PROFILIN 12 | ECU06_1350-m1 ROSETTAFOLD 1YPR A 0.4623 2.0715 0.1250 112 125 pdb1ypr.ent.gz PROFILIN 13 | ECU06_1350-m1 ROSETTAFOLD 1YPR B 0.4515 2.0896 0.1351 111 125 pdb1ypr.ent.gz PROFILIN 14 | ECU06_1350-m1 ROSETTAFOLD 5ZZA P 0.4514 2.2460 0.1261 111 119 pdb5zza.ent.gz UNCHARACTERIZED PROTEIN 15 | 16 | ### ECU08_1425; Top matches across all predictors. Sorted by q-scores: duplicated RCSB PDB entries are not shown 17 | ECU08_1425-m1 ROSETTAFOLD 3K0X A 0.5951 1.8115 0.1163 86 99 pdb3k0x.ent.gz PROTEIN TEN1 18 | ECU08_1425-m1 ROSETTAFOLD 5DOI H 0.5879 1.7411 0.1098 82 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 19 | ECU08_1425-m1 ROSETTAFOLD 5DOI F 0.5875 1.7431 0.1098 82 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 20 | ECU08_1425-m1 ROSETTAFOLD 5DOI G 0.5790 1.7088 0.1235 81 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 21 | ECU08_1425-m1 ROSETTAFOLD 5DOI E 0.5768 1.8061 0.1098 82 93 pdb5doi.ent.gz TELOMERASE ASSOCIATED PROTEIN P45 22 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Homology/LOGS/GESAMT_ALPHAFOLD_2021-09-15.log: -------------------------------------------------------------------------------- 1 | 2 | VERSION: 0.5e 3 | COMMAND LINE: run_GESAMT.pl -cpu 20 -query -arch /media/Data_3/databases/3DFI/RCSB_GESAMT -input RESULTS_20210915//Folding/ALPHAFOLD_3D_Parsed/ECU03_1140-m1.pdb RESULTS_20210915//Folding/ALPHAFOLD_3D_Parsed/ECU03_1140-m2.pdb RESULTS_20210915//Folding/ALPHAFOLD_3D_Parsed/ECU03_1140-m3.pdb RESULTS_20210915//Folding/ALPHAFOLD_3D_Parsed/ECU03_1140-m4.pdb RESULTS_20210915//Folding/ALPHAFOLD_3D_Parsed/ECU03_1140-m5.pdb RESULTS_20210915//Folding/ALPHAFOLD_3D_Parsed/ECU06_1350-m1.pdb RESULTS_20210915//Folding/ALPHAFOLD_3D_Parsed/ECU06_1350-m2.pdb RESULTS_20210915//Folding/ALPHAFOLD_3D_Parsed/ECU06_1350-m3.pdb RESULTS_20210915//Folding/ALPHAFOLD_3D_Parsed/ECU06_1350-m4.pdb RESULTS_20210915//Folding/ALPHAFOLD_3D_Parsed/ECU06_1350-m5.pdb RESULTS_20210915//Folding/ALPHAFOLD_3D_Parsed/ECU08_1425-m1.pdb RESULTS_20210915//Folding/ALPHAFOLD_3D_Parsed/ECU08_1425-m2.pdb RESULTS_20210915//Folding/ALPHAFOLD_3D_Parsed/ECU08_1425-m3.pdb RESULTS_20210915//Folding/ALPHAFOLD_3D_Parsed/ECU08_1425-m4.pdb RESULTS_20210915//Folding/ALPHAFOLD_3D_Parsed/ECU08_1425-m5.pdb -o RESULTS_20210915//Homology/GESAMT/ALPHAFOLD -l RESULTS_20210915//Homology/LOGS/GESAMT_ALPHAFOLD_2021-09-15.log -mode normal -z 4 | Started on: Wed Sep 15 15:45:02 2021 5 | Completed on: Wed Sep 15 16:04:30 2021 6 | Total run time: 19.47 minutes 7 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Homology/LOGS/GESAMT_ALPHAFOLD_2021-09-15_descriptive_matches.err: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PombertLab/3DFI/e4e0eb13e01393aa0cc4214b48860e80167a472e/Examples/Results_3DFI/Homology/LOGS/GESAMT_ALPHAFOLD_2021-09-15_descriptive_matches.err -------------------------------------------------------------------------------- /Examples/Results_3DFI/Homology/LOGS/GESAMT_RAPTORX_2021-09-15.log: -------------------------------------------------------------------------------- 1 | 2 | VERSION: 0.5e 3 | COMMAND LINE: run_GESAMT.pl -cpu 20 -query -arch /media/Data_3/databases/3DFI/RCSB_GESAMT -input RESULTS_20210915//Folding/RAPTORX_3D/PDB/ECU03_1140-m1.pdb RESULTS_20210915//Folding/RAPTORX_3D/PDB/ECU03_1140-m2.pdb RESULTS_20210915//Folding/RAPTORX_3D/PDB/ECU03_1140-m3.pdb RESULTS_20210915//Folding/RAPTORX_3D/PDB/ECU03_1140-m4.pdb RESULTS_20210915//Folding/RAPTORX_3D/PDB/ECU03_1140-m5.pdb RESULTS_20210915//Folding/RAPTORX_3D/PDB/ECU06_1350-m1.pdb RESULTS_20210915//Folding/RAPTORX_3D/PDB/ECU06_1350-m2.pdb RESULTS_20210915//Folding/RAPTORX_3D/PDB/ECU06_1350-m3.pdb RESULTS_20210915//Folding/RAPTORX_3D/PDB/ECU06_1350-m4.pdb RESULTS_20210915//Folding/RAPTORX_3D/PDB/ECU06_1350-m5.pdb RESULTS_20210915//Folding/RAPTORX_3D/PDB/ECU08_1425-m1.pdb RESULTS_20210915//Folding/RAPTORX_3D/PDB/ECU08_1425-m2.pdb RESULTS_20210915//Folding/RAPTORX_3D/PDB/ECU08_1425-m3.pdb RESULTS_20210915//Folding/RAPTORX_3D/PDB/ECU08_1425-m4.pdb RESULTS_20210915//Folding/RAPTORX_3D/PDB/ECU08_1425-m5.pdb -o RESULTS_20210915//Homology/GESAMT/RAPTORX -l RESULTS_20210915//Homology/LOGS/GESAMT_RAPTORX_2021-09-15.log -mode normal -z 4 | Started on: Wed Sep 15 16:08:23 2021 5 | Completed on: Wed Sep 15 16:27:32 2021 6 | Total run time: 19.15 minutes 7 | -------------------------------------------------------------------------------- /Examples/Results_3DFI/Homology/LOGS/GESAMT_RAPTORX_2021-09-15_descriptive_matches.err: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PombertLab/3DFI/e4e0eb13e01393aa0cc4214b48860e80167a472e/Examples/Results_3DFI/Homology/LOGS/GESAMT_RAPTORX_2021-09-15_descriptive_matches.err -------------------------------------------------------------------------------- /Examples/Results_3DFI/Homology/LOGS/GESAMT_ROSETTAFOLD_2021-09-15.log: -------------------------------------------------------------------------------- 1 | 2 | VERSION: 0.5e 3 | COMMAND LINE: run_GESAMT.pl -cpu 20 -query -arch /media/Data_3/databases/3DFI/RCSB_GESAMT -input 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.//Visualization/ALPHAFOLD/ECU06_1350-m5/ECU06_1350-m5.pdb 11 | .//Visualization/ALPHAFOLD/ECU08_1425-m1/ECU08_1425-m1.pdb 12 | .//Visualization/ALPHAFOLD/ECU08_1425-m2/ECU08_1425-m2.pdb 13 | .//Visualization/ALPHAFOLD/ECU08_1425-m3/ECU08_1425-m3.pdb 14 | .//Visualization/ALPHAFOLD/ECU08_1425-m4/ECU08_1425-m4.pdb 15 | .//Visualization/ALPHAFOLD/ECU08_1425-m5/ECU08_1425-m5.pdb 16 | .//Visualization/ROSETTAFOLD/ECU03_1140-m1/ECU03_1140-m1.pdb 17 | .//Visualization/ROSETTAFOLD/ECU06_1350-m1/ECU06_1350-m1.pdb 18 | .//Visualization/ROSETTAFOLD/ECU08_1425-m1/ECU08_1425-m1.pdb 19 | .//Visualization/RAPTORX/ECU03_1140-m3/ECU03_1140-m3.pdb 20 | .//Visualization/RAPTORX/ECU03_1140-m2/ECU03_1140-m2.pdb 21 | .//Visualization/RAPTORX/ECU03_1140-m1/ECU03_1140-m1.pdb 22 | .//Visualization/RAPTORX/ECU03_1140-m5/ECU03_1140-m5.pdb 23 | .//Visualization/RAPTORX/ECU03_1140-m4/ECU03_1140-m4.pdb 24 | .//Visualization/RAPTORX/ECU06_1350-m3/ECU06_1350-m3.pdb 25 | .//Visualization/RAPTORX/ECU06_1350-m4/ECU06_1350-m4.pdb 26 | .//Visualization/RAPTORX/ECU06_1350-m5/ECU06_1350-m5.pdb 27 | .//Visualization/RAPTORX/ECU06_1350-m2/ECU06_1350-m2.pdb 28 | .//Visualization/RAPTORX/ECU06_1350-m1/ECU06_1350-m1.pdb 29 | .//Visualization/RAPTORX/ECU08_1425-m5/ECU08_1425-m5.pdb 30 | .//Visualization/RAPTORX/ECU08_1425-m4/ECU08_1425-m4.pdb 31 | .//Visualization/RAPTORX/ECU08_1425-m2/ECU08_1425-m2.pdb 32 | .//Visualization/RAPTORX/ECU08_1425-m3/ECU08_1425-m3.pdb 33 | .//Visualization/RAPTORX/ECU08_1425-m1/ECU08_1425-m1.pdb 34 | -------------------------------------------------------------------------------- /Homology_search/PDB_headers.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab 2020 3 | my $version = '0.4b'; 4 | my $name = 'PDB_headers.pl'; 5 | my $updated = '2022-02-23'; 6 | 7 | use strict; 8 | use warnings; 9 | use Getopt::Long qw(GetOptions); 10 | use File::Basename; 11 | use File::Find; 12 | use PerlIO::gzip; 13 | 14 | ## Usage definition 15 | my $USAGE = <<"OPTIONS"; 16 | NAME ${name} 17 | VERSION ${version} 18 | UPDATED ${updated} 19 | SYNOPSIS Generates a Tab-delimited list of PDB structures, their titles and 20 | chains from the PDB files headers 21 | 22 | REQUIREMENTS PDB files downloaded from RCSB PDB; e.g. pdb2zvl.ent.gz 23 | PerlIO::gzip 24 | 25 | USAGE EXAMPLE ${name} \\ 26 | -p RCSB_PDB/ RCSB_PDB_obsolete/\\ 27 | -o RCSB_PDB_titles.tsv \\ 28 | -v 1000 29 | 30 | OPTIONS: 31 | -p (--pdb) Directories containing PDB files downloaded from RCSB PDB/PDBe (gzipped) 32 | -o (--output) Output file in tsv format 33 | -f (--force) Regenerate all PDB titles ## Default off 34 | -v (--verbose) Prints progress every X file [Default: 1000] 35 | OPTIONS 36 | die "\n$USAGE\n" unless @ARGV; 37 | 38 | ## Defining options 39 | my @pdbs; 40 | my $rcsb_list; 41 | my $force; 42 | my $verbose = 1000; 43 | GetOptions( 44 | 'p|pdb=s@{1,}' => \@pdbs, 45 | 'o|output=s' => \$rcsb_list, 46 | 'f|force' => \$force, 47 | 'v|verbose=i' => \$verbose 48 | ); 49 | 50 | 51 | ## Recursing through PDB directory 52 | my @pdb; 53 | for my $dir (@pdbs){ 54 | find( 55 | sub { push @pdb, $File::Find::name unless -d; }, 56 | $dir 57 | ); 58 | } 59 | 60 | ## Doing a first pass to see which files have been parsed previously 61 | ## Should reduce overall computation time by skipping parsing 62 | my %previous_data; 63 | my $diamond = '>'; 64 | unless ($force){ 65 | if (-f $rcsb_list){ 66 | $diamond = '>>'; 67 | open LIST, "<", "$rcsb_list" or die "Can't read $rcsb_list: $!\n"; 68 | while (my $line = ){ 69 | chomp $line; 70 | if ($line =~ /^(\w+)/){ 71 | my $rcsb_entry = $1; 72 | $previous_data{$rcsb_entry} = 1; 73 | } 74 | } 75 | close LIST; 76 | } 77 | } 78 | 79 | ## Parsing PDB files (*.ent.gz) 80 | open OUT, "$diamond", "$rcsb_list" or die "Can't create file $rcsb_list: $!\n"; 81 | 82 | my $pdb_count = 0; 83 | my $start = time; 84 | while (my $pb = shift@pdb){ 85 | 86 | if ($pb =~ /.ent.gz$/){ ## skipping other files if present 87 | 88 | $pdb_count++; 89 | 90 | ## Grabbing RCSB PDB entry name from pdb file 91 | my ($pdb, $folder) = fileparse($pb); 92 | $pdb =~ s/^pdb//; 93 | $pdb =~ s/.ent.gz$//; 94 | 95 | ## verbosity; lots of files to parse... 96 | my $modulo = ($pdb_count % $verbose); 97 | my $current_count = commify($pdb_count); 98 | if ($modulo == 0){ print "Working on PDB file # $current_count: $pb\n"; } 99 | 100 | ## Working on PDB if is has not been seen before 101 | if (exists $previous_data{$pdb}) { next; } 102 | else { 103 | open PDB, "<:gzip", "$pb" or die "Can't open file $pb: $!\n"; 104 | my $title = undef; 105 | my %molecules; 106 | my $mol_id = undef; 107 | 108 | while (my $line = ){ 109 | chomp $line; 110 | ## Getting title info from TITLE entries 111 | if ($line =~ /^TITLE\s{5}(.*)$/){ 112 | my $key = $1; 113 | $key =~ s/\s+$/ /; ## Discard trailing space characters 114 | $title .= $key; 115 | } 116 | elsif ($line =~ /^TITLE\s+\d+\s(.*)$/){ 117 | my $key = $1; 118 | $key =~ s/\s+$/ /; ## Discard trailing space characters 119 | $title .= $key; 120 | } 121 | ## Getting chain information from COMPND entries 122 | elsif ($line =~ /^COMPND\s+(\d+)?\s?MOL_ID:\s(\d+)/){ 123 | $mol_id = $2; 124 | } 125 | elsif ($line =~ /^COMPND\s+(\d+)?(.*)$/){ 126 | my $data = $2; 127 | $data =~ s/\s+$//; 128 | if ($mol_id){ 129 | $molecules{$mol_id} .= $data; 130 | } 131 | else { 132 | print STDERR "[W] $pdb is missing a molecule ID\n"; 133 | } 134 | } 135 | } 136 | binmode PDB, ":gzip(none)"; 137 | 138 | ## Printing title 139 | if (defined $title){ 140 | print OUT "$pdb\tTITLE\t$title\n"; 141 | } 142 | else{ 143 | print STDERR "[W] $pdb is missing a title\n"; 144 | } 145 | 146 | ## Printing chain(s) 147 | foreach my $id (sort (keys %molecules)){ 148 | 149 | my $molecule; 150 | my $chains; 151 | 152 | if ($molecules{$id} =~ /MOLECULE: (.*?);/){ 153 | $molecule = $1; 154 | } 155 | elsif($molecules{$id} =~ /MOLECULE: (.*?)/){ 156 | $molecule = $1; 157 | ## If at end of COMPND section, no semicolon to after the molecule(s) 158 | } 159 | 160 | if ($molecules{$id} =~ /CHAIN: (.*?);/){ 161 | $chains = $1; 162 | } 163 | elsif ($molecules{$id} =~ /CHAIN: (.*\w)/){ 164 | $chains = $1; 165 | ## If at end of COMPND section, no semicolon to after the chain(s) 166 | } 167 | 168 | my @chains; 169 | if(defined $chains){ 170 | $chains =~ s/ //g; 171 | @chains = split (",", $chains); 172 | foreach my $chain (@chains){ 173 | if (defined $molecule){ print OUT "$pdb\t$chain\t$molecule\n"; } 174 | ## Molecules might not be defined if engineered 175 | else { 176 | print OUT "$pdb\t$chain\tundefined molecule\n"; 177 | } 178 | } 179 | } 180 | else{ 181 | print STDERR "[W] $pdb is missing a chain\n"; 182 | } 183 | } 184 | } 185 | } 186 | } 187 | 188 | my $final_count = commify($pdb_count); 189 | my $run_time = (time - $start)/60; 190 | $run_time = sprintf ("%.2f", $run_time); 191 | print "\nIterated through a total of $final_count PDB files\n"; 192 | print "Job completed in $run_time minutes.\n\n"; 193 | 194 | ### Subroutine(s) 195 | sub commify { 196 | my $text = reverse $_[0]; 197 | $text =~ s/(\d\d\d)(?=\d)(?!\d*\.)/$1,/g; 198 | return scalar reverse $text; 199 | } -------------------------------------------------------------------------------- /Homology_search/parse_all_models_by_Q.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab, Illinois Tech, 2021 3 | my $name = 'parse_all_models_by_Q.pl'; 4 | my $version = '0.2'; 5 | my $updated = '2022-04-27'; 6 | 7 | use strict; 8 | use warnings; 9 | use Getopt::Long qw(GetOptions); 10 | use File::Basename; 11 | 12 | my $usage = <<"USAGE"; 13 | NAME ${name} 14 | VERSION ${version} 15 | UPDATED ${updated} 16 | SYNOPSIS Parses the output of descriptive_GESAMT_matches.pl per protein accross all models, 17 | from best Q-score to worst. 18 | 19 | EXAMPLE ${name} \\ 20 | -a gesamt \\ 21 | -m *_GESAMT_per_model.matches \\ 22 | -o All_GESAMT_matches_per_protein.tsv \\ 23 | -x 50 24 | 25 | GENERAL OPTIONS: 26 | -a (--align) Alignment tool: gesamt or foldseek [Default: gesamt] 27 | -m (--matches) Foldseek/GESAMT matches parsed by descriptive_matches.pl 28 | -o (--out) Output file in TSV format [Default: All_GESAMT_matches_per_protein.tsv] 29 | -x (--max) Max number of distinct RCSB/chain hits to keep [Default: 50] 30 | -r (--redun) Keep all entries for redundant RCSB chains [Default: off] 31 | -w (--word) Use word regular expression (\\w+) to capture locus tag [Default: off] 32 | USAGE 33 | die "\n$usage\n" unless @ARGV; 34 | 35 | my $aligner = 'gesamt'; 36 | my @matches; 37 | my $outfile = 'All_GESAMT_matches_per_protein.tsv'; 38 | my $max = 50; 39 | my $redundancy; 40 | my $word; 41 | GetOptions( 42 | 'a|align=s' => \$aligner, 43 | 'm|matches=s@{1,}' => \@matches, 44 | 'o|out=s' => \$outfile, 45 | 'x|max=i' => \$max, 46 | 'r|redun' => \$redundancy, 47 | 'w|word' => \$word 48 | ); 49 | 50 | ## Output file 51 | open OUT, ">", "$outfile" or die "Can't create $outfile: $!\n"; 52 | 53 | 54 | ## ## Store proteins and corresponding matches in a single database 55 | my %proteins; 56 | while (my $file = shift@matches){ 57 | open IN, "<", "$file"; 58 | 59 | ## Grabbing the predictor used from the filename 60 | my $filename = fileparse($file); 61 | my $predictor; 62 | if ($aligner eq 'gesamt'){ 63 | ($predictor) = $filename =~ /^(\w+)_GESAMT_per_(\w+).matches/; 64 | } 65 | elsif ($aligner eq 'foldseek'){ 66 | ($predictor) = $filename =~ /^(\w+)_FOLDSEEK_per_(\w+).matches/; 67 | } 68 | 69 | ## 70 | while (my $line = ){ 71 | chomp $line; 72 | if ($line =~ /^#/){ next; } 73 | elsif ($line eq ''){ next; } 74 | else { 75 | my @data = split ("\t", $line); 76 | my $protein; 77 | if ($word){ ($protein) = $data[0] =~ /^(\w+)/; } 78 | else { ($protein) = $data[0] =~ /^(\S+)\-\w\d+$/; } 79 | 80 | ## Tagging the line with the predictor used 81 | my $newline = $line."\t"."$predictor"; 82 | 83 | ## Add line to @array containing all matches found for the corresponding protein 84 | push (@{$proteins{$protein}}, $newline); 85 | } 86 | } 87 | } 88 | 89 | ## Iterating through all proteins 90 | for my $protein (sort (keys %proteins)){ 91 | 92 | my %rcsb_matches; 93 | my $hit_counter; 94 | 95 | print OUT "\n### $protein; Top matches across all predictors. Sorted by quality scores: "; 96 | if ($redundancy){ print OUT "duplicated RCSB PDB entries (if any) are shown\n"; } 97 | else { print OUT "duplicated RCSB PDB entries are not shown\n"; } 98 | 99 | ## Sorting by column 100 | my @sorted_matches; 101 | if ($aligner eq 'gesamt'){ 102 | ## Q-score is located in column #5 103 | @sorted_matches = sort { (split("\t", $b))[4] <=> (split("\t", $a))[4] } @{$proteins{$protein}}; 104 | } 105 | if ($aligner eq 'foldseek'){ 106 | ## Q-score is located in column #12 107 | @sorted_matches = sort { (split("\t", $b))[11] <=> (split("\t", $a))[11] } @{$proteins{$protein}}; 108 | } 109 | 110 | while (my $line = shift@sorted_matches){ 111 | 112 | my @data = split ("\t", $line); 113 | my $predictor = pop(@data); 114 | my $rcsb_id; 115 | my $rcsb_chain; 116 | if ($aligner eq 'gesamt'){ 117 | $rcsb_id = $data[2]; 118 | $rcsb_chain = $data[3]; 119 | } 120 | elsif ($aligner eq 'foldseek'){ 121 | if ($data[1] =~ /^pdb(\w{4}).ent.gz_(\S+)$/){ 122 | $rcsb_id = $1; 123 | $rcsb_chain = $2; 124 | } 125 | elsif ($data[1] =~ /^pdb(\w{4}).ent.gz$/){ 126 | $rcsb_id = $1; 127 | $rcsb_chain = 'A'; 128 | } 129 | } 130 | 131 | ## Adding chain to RCSB tag, a unique ID often contain more than one protein or chain 132 | my $rcsb_key = "$rcsb_id".'_'."$rcsb_chain"; 133 | 134 | if ($aligner eq 'gesamt'){ 135 | ## Replacing uninformative column by $predictor 136 | $data[1] = $predictor; 137 | } 138 | if ($aligner eq 'foldseek'){ 139 | ## Adding $predictor to @data with splice 140 | splice (@data, 1, 0, $predictor); 141 | } 142 | 143 | if ($redundancy){ ## Keeping redundant RCSB tag + chain if redundancy is wanted 144 | $rcsb_matches{$rcsb_key} = ''; 145 | $hit_counter += 1; 146 | } 147 | else { ## Checking if the same RCSB tag + chain if found, if so skip 148 | if (exists $rcsb_matches{$rcsb_key}){ next; } 149 | else { 150 | $rcsb_matches{$rcsb_key} = ''; 151 | $hit_counter += 1; 152 | } 153 | } 154 | 155 | if ($hit_counter <= $max){ 156 | for (0..$#data-1){ print OUT "$data[$_]\t";} 157 | print OUT "$data[$#data]\n"; 158 | } 159 | } 160 | } 161 | -------------------------------------------------------------------------------- /Homology_search/run_GESAMT.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab 2020 3 | my $version = '0.5f'; 4 | my $name = 'run_GESAMT.pl'; 5 | my $updated = '2021-12-21'; 6 | 7 | use strict; 8 | use warnings; 9 | use File::Find; 10 | use File::Basename; 11 | use File::Path qw(make_path); 12 | use POSIX 'strftime'; 13 | use Getopt::Long qw(GetOptions); 14 | 15 | my @command = @ARGV; ## Keeping track of command line for log 16 | 17 | ## Usage definition 18 | my $USAGE = <<"OPTIONS"; 19 | NAME ${name} 20 | VERSION ${version} 21 | UPDATED ${updated} 22 | SYNOPSIS Run GESAMT structural searches against PDB structures 23 | REQUIREMENTS PDB files downloaded from RCSB PDB; e.g. pdb2zvl.ent.gz 24 | GESAMT; see https://www.ccp4.ac.uk/ 25 | 26 | CREATE DB ${name} -cpu 10 -make -arch /media/Data_2/GESAMT_ARCHIVE -pdb /media/Data_2/PDB/ 27 | UPDATE DB ${name} -cpu 10 -update -arch /media/Data_2/GESAMT_ARCHIVE -pdb /media/Data_2/PDB/ 28 | QUERY DB ${name} -cpu 10 -query -arch /media/Data_2/GESAMT_ARCHIVE -input *.pdb -o ./ -mode normal 29 | 30 | OPTIONS: 31 | -c (--cpu) CPU threads [Default: 10] 32 | -a (--arch) GESAMT archive location [Default: ./] 33 | -l (--log) Log file [Default: GESAMT.log] 34 | 35 | ## Creating/updating a GESAMT archive 36 | -m (--make) Create a GESAMT archive 37 | -u (--update) Update existing archive 38 | -p (--pdb) Folder containing RCSB PDB files to archive 39 | 40 | ## Querying a GESAMT archive 41 | -q (--query) Query a GESAMT archive 42 | -i (--input) PDF files to query 43 | -o (--outdir) Output directory [Default: ./] 44 | -d (--mode) Query mode: normal of high [Default: normal] 45 | -z (--gzip) Compress output files [Default: off] 46 | 47 | ## References 48 | 1) Enhanced fold recognition using efficient short fragment clustering. 49 | Krissinel E. J Mol Biochem. 2012;1(2):76-85. PMID: 27882309 PMCID: PMC5117261 50 | 51 | 2) Overview of the CCP4 suite and current developments 52 | Winn MD et al. Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-42. PMID: 21460441 PMCID: PMC3069738 DOI: 10.1107/S0907444910045749 53 | OPTIONS 54 | die "\n$USAGE\n" unless @ARGV; 55 | 56 | ## Defining options 57 | my $cpu = 10; 58 | my $arch = './'; 59 | my $log = 'GESAMT.log'; 60 | my $make; 61 | my $update; 62 | my $pdb; 63 | my $query; 64 | my @input; 65 | my $outdir = './'; 66 | my $mode = 'normal'; 67 | my $gnuzip; 68 | GetOptions( 69 | 'c|cpu=i' => \$cpu, 70 | 'a|arch=s' => \$arch, 71 | 'l|log=s' => \$log, 72 | 'm|make' => \$make, 73 | 'u|update' => \$update, 74 | 'p|pdb=s' => \$pdb, 75 | 'q|query' => \$query, 76 | 'i|input=s@{1,}' => \@input, 77 | 'o|outdir=s' => \$outdir, 78 | 'd|mode=s' => \$mode, 79 | 'z|gzip' => \$gnuzip 80 | ); 81 | 82 | ## Creating log 83 | my $date = strftime '%Y-%m-%d', localtime; 84 | my $start = localtime(); 85 | my $tstart = time; 86 | open LOG, ">>", "$log" or die "Can't create log file $log: $!\n"; 87 | print LOG "\nVERSION: $version\n"."COMMAND LINE: $name @command\n"; 88 | print LOG "Started on: $start\n"; 89 | 90 | ## Program check 91 | my $prog = `echo \$(command -v gesamt)`; 92 | chomp $prog; 93 | if ($prog eq ''){ 94 | die "\nERROR: Cannot find gesamt. Please install GESAMT in your path\n\n"; 95 | } 96 | 97 | ## Checking for unknown task 98 | if (!defined $update and !defined $make and !defined $query){ 99 | die "\nUnknown task. Please specify -make, -update or -query on the command line.\n\n"; 100 | } 101 | 102 | ## Creating/updating GESAMT archive 103 | unless (-d $arch){ 104 | make_path ($arch, {mode => 0755}) or die "Can't create folder $arch: $!\n"; 105 | } 106 | 107 | if ($update){ 108 | system ("gesamt \\ 109 | --update-archive $arch \\ 110 | -pdb $pdb \\ 111 | -nthreads=$cpu") == 0 or checksig(); 112 | } 113 | elsif ($make){ 114 | system ("gesamt \\ 115 | --make-archive $arch \\ 116 | -pdb $pdb \\ 117 | -nthreads=$cpu") == 0 or checksig(); 118 | } 119 | 120 | ## Running GESAMT queries/Skipping previously done searches 121 | unless (-d $outdir){ 122 | make_path ($outdir, {mode => 0755}) or die "Can't create folder $outdir: $!\n"; 123 | } 124 | 125 | my @gsm; 126 | my %results; 127 | find (sub {push @gsm, $File::Find::name unless -d}, $outdir); 128 | 129 | while (my $gsm = shift(@gsm)){ 130 | my ($result, $folder) = fileparse($gsm); 131 | if ($gnuzip){ $result =~ s/\.\w+\.gesamt.gz$//; } 132 | else { $result =~ s/\.\w+\.gesamt$//; } 133 | $results{$result} = 'done'; 134 | } 135 | 136 | if ($query){ 137 | while (my $file = shift(@input)){ 138 | my ($pdb, $dir) = fileparse($file); 139 | $pdb =~ s/.pdb$//; 140 | unless (exists $results{$pdb}){ 141 | system ("gesamt $file \\ 142 | -archive $arch \\ 143 | -nthreads=$cpu \\ 144 | -$mode \\ 145 | -o $outdir/$pdb.$mode.gesamt") == 0 or checksig(); 146 | 147 | if ($gnuzip){ 148 | ## Compressing data with GZIP to save some space 149 | print "\n Compressing $outdir/$pdb.$mode.gesamt with GZIP ...\n"; 150 | system "gzip $outdir/$pdb.$mode.gesamt"; 151 | } 152 | } 153 | ## Searches can take a while, best to skip if done previously 154 | else { 155 | print "Skipping PDB file: $pdb => GESAMT result found in output directory $outdir\n"; 156 | } 157 | } 158 | } 159 | 160 | my $end = localtime(); 161 | my $endtime = (time - $tstart)/60; 162 | $endtime = sprintf ("%.2f", $endtime); 163 | print LOG "Completed on: $end\n"; 164 | print LOG "Total run time: $endtime minutes\n"; 165 | close LOG; 166 | 167 | ### Subroutine(s) 168 | sub checksig { 169 | 170 | my $exit_value = $?; 171 | my $modulo = $exit_value % 255; 172 | 173 | if ($modulo == 2) { 174 | print "\n\nSIGINT detected: Ctrl+C. Exiting...\n"; 175 | exit(1); 176 | } 177 | elsif ($modulo == 131) { 178 | print "\n\nSIGTERM detected: Ctrl+\\. Exiting...\n"; 179 | exit(1); 180 | } 181 | 182 | } -------------------------------------------------------------------------------- /Homology_search/run_foldseek.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab 2022 3 | my $version = '0.2'; 4 | my $name = 'run_foldseek.pl'; 5 | my $updated = '2022-04-28'; 6 | 7 | use strict; 8 | use warnings; 9 | use File::Find; 10 | use File::Basename; 11 | use File::Path qw(make_path); 12 | use POSIX 'strftime'; 13 | use Getopt::Long qw(GetOptions); 14 | 15 | my @command = @ARGV; ## Keeping track of command line for log 16 | 17 | ## Usage definition 18 | my $USAGE = <<"OPTIONS"; 19 | NAME ${name} 20 | VERSION ${version} 21 | UPDATED ${updated} 22 | SYNOPSIS Run foldseek searches against PDB structures 23 | 24 | REQUIREMENTS Foldseek - https://github.com/steineggerlab/foldseek 25 | 26 | CREATE DB ${name} -create -db /media/Data_2/FSEEK/rcsb -pdb /media/Data_2/PDB/ 27 | QUERY DB ${name} -query -db /media/Data_2/FSEEK/rcsb -input *.pdb -o ./FSEEK_RESULTS -z 28 | 29 | OPTIONS: 30 | -d (--db) Foldseek database to create or query 31 | -t (--threads) CPU threads [Default: 12] 32 | -v (--verbosity) Verbosity: 0: quiet, 1: +errors, 2: +warnings, 3: +info [Default: 3] 33 | -l (--log) Log file [Default: foldseek.log] 34 | 35 | ## Creating a Foldseek database 36 | -c (--create) Create a foldseek database 37 | -p (--pdb) Folder containing the PDB files for the database 38 | 39 | ## Querying a Foldseek database 40 | -q (--query) Query a Foldseek database 41 | -o (--outdir) Output directory [Default: ./] 42 | -i (--input) PDF files to query 43 | -a (--atype) Alignment type [Default: 2]: 44 | 0: 3Di Gotoh-Smith-Waterman 45 | 1: TMalign 46 | 2: 3Di+AA Gotoh-Smith-Waterman 47 | -m (--mseq) Amount of prefilter sequences handed to the alignment [Default: 300] 48 | -z (--gzip) Compress output files [Default: off] 49 | 50 | ## Reference 51 | van Kempen M, Kim S, Tumescheit C, Mirdita M, Söding J, and Steinegger M. 52 | Foldseek: fast and accurate protein structure search. bioRxiv, 53 | doi:10.1101/2022.02.07.479398 (2022) 54 | OPTIONS 55 | die "\n$USAGE\n" unless @ARGV; 56 | 57 | ## Defining options 58 | my $db; 59 | my $threads = 12; 60 | my $verbosity = 3; 61 | my $log = 'foldseek.log'; 62 | 63 | my $create; 64 | my $pdb; 65 | 66 | my $query; 67 | my $outdir = './'; 68 | my @input; 69 | my $atype = 2; 70 | my $mseqs = 300; 71 | my $gnuzip; 72 | GetOptions( 73 | 'd|db=s' => \$db, 74 | 'l|log=s' => \$log, 75 | 't|threads=i' => \$threads, 76 | 'v|verbosity=i' => \$verbosity, 77 | 'c|create' => \$create, 78 | 'p|pdb=s' => \$pdb, 79 | 'q|query' => \$query, 80 | 'o|outdir=s' => \$outdir, 81 | 'a|atype=i' => \$atype, 82 | 'm|mseq=i' => \$mseqs, 83 | 'i|input=s@{1,}' => \@input, 84 | 'z|gzip' => \$gnuzip 85 | ); 86 | 87 | ## Creating log 88 | my $date = strftime '%Y-%m-%d', localtime; 89 | my $start = localtime(); 90 | my $tstart = time; 91 | open LOG, ">>", "$log" or die "Can't create log file $log: $!\n"; 92 | print LOG "\nVERSION: $version\n"."COMMAND LINE: $name @command\n"; 93 | print LOG "Started on: $start\n"; 94 | 95 | ## Program check 96 | my $prog = `echo \$(command -v foldseek)`; 97 | chomp $prog; 98 | if ($prog eq ''){ 99 | die "\nERROR: Cannot find foldseek. Please install foldseek in your path\n\n"; 100 | } 101 | 102 | ## Checking for unknown task 103 | if (!defined $create and !defined $query){ 104 | die "\nUnknown task. Please specify -create or -query on the command line.\n\n"; 105 | } 106 | 107 | ## Creating a foldseek database 108 | if ($create){ 109 | 110 | unless ($pdb){ 111 | die "\nERROR: Please enter folder containing the PDB files for the database."; 112 | } 113 | 114 | my ($dbname,$dbpath) = fileparse($db); 115 | unless (-d $dbpath){ 116 | make_path( $dbpath, { mode => 0755 } ) or die "Can't create folder $dbpath: $!\n"; 117 | } 118 | 119 | system ("foldseek \\ 120 | createdb \\ 121 | --threads $threads \\ 122 | $pdb \\ 123 | $db") == 0 or checksig(); 124 | } 125 | 126 | ## Running foldseek queries/Skipping previously done searches 127 | if ($query){ 128 | 129 | unless (-d $outdir){ 130 | mkdir ($outdir, 0755) or die "Can't create folder $outdir: $!\n"; 131 | } 132 | 133 | my @fsk; 134 | my %results; 135 | find (sub {push @fsk, $File::Find::name unless -d}, $outdir); 136 | 137 | while (my $fsk = shift(@fsk)){ 138 | my ($result, $folder) = fileparse($fsk); 139 | if ($gnuzip){ $result =~ s/\.fseek.gz$//; } 140 | else { $result =~ s/\.fseek$//; } 141 | $results{$result} = 'done'; 142 | } 143 | 144 | while (my $file = shift(@input)){ 145 | 146 | my ($pdb, $dir) = fileparse($file); 147 | $pdb =~ s/.pdb$//; 148 | 149 | unless (exists $results{$pdb}){ 150 | 151 | print "\n Running foldseek on $file...\n"; 152 | 153 | system ("foldseek \\ 154 | easy-search \\ 155 | --max-seqs $mseqs \\ 156 | --alignment-type $atype \\ 157 | --threads $threads \\ 158 | -v $verbosity \\ 159 | $file \\ 160 | $db \\ 161 | $outdir/$pdb.fseek \\ 162 | $outdir/tmp") == 0 or checksig(); 163 | 164 | if ($gnuzip){ 165 | ## Compressing data with GZIP to save some space 166 | print "\n Compressing $outdir/$pdb.fseek with GZIP ...\n"; 167 | system "gzip $outdir/$pdb.fseek"; 168 | } 169 | } 170 | 171 | ## Searches can take a while, best to skip if done previously 172 | else { 173 | print " Skipping PDB file: $pdb => Foldseek result found in output directory $outdir\n"; 174 | } 175 | } 176 | 177 | ## Delete tmp directory 178 | if (-d "$outdir/tmp"){ system "rm -R $outdir/tmp"; } 179 | } 180 | 181 | my $end = localtime(); 182 | my $endtime = (time - $tstart)/60; 183 | $endtime = sprintf ("%.2f", $endtime); 184 | print LOG "Completed on: $end\n"; 185 | print LOG "Total run time: $endtime minutes\n"; 186 | close LOG; 187 | 188 | ### Subroutine(s) 189 | sub checksig { 190 | 191 | my $exit_code = $?; 192 | my $modulo = $exit_code % 255; 193 | 194 | print "\nExit code = $exit_code; modulo = $modulo \n"; 195 | 196 | if ($modulo == 2) { 197 | print "\nSIGINT detected: Ctrl+C => exiting...\n"; 198 | exit(2); 199 | } 200 | elsif ($modulo == 131) { 201 | print "\nSIGTERM detected: Ctrl+\\ => exiting...\n"; 202 | exit(131); 203 | } 204 | 205 | } -------------------------------------------------------------------------------- /Homology_search/update_PDB.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab 2021 3 | my $version = '0.3'; 4 | my $name = 'update_PDB.pl'; 5 | my $updated = '2022-02-23'; 6 | 7 | use strict; 8 | use warnings; 9 | use Getopt::Long qw(GetOptions); 10 | 11 | ## Usage definition 12 | my $USAGE = <<"OPTIONS"; 13 | NAME ${name} 14 | VERSION ${version} 15 | UPDATED ${updated} 16 | SYNOPSIS Downloads/updates the RCSB PDB database with rsync 17 | 18 | COMMAND ${name} \\ 19 | -o ./PDB \\ 20 | -d current \\ 21 | -n 15 22 | 23 | OPTIONS: 24 | -o (--outdir) PDB output directory [Default: PDB] 25 | -n (--nice) Defines niceness (adjusts scheduling priority) 26 | -v (--verbose) Adds verbosity 27 | -d (--data) Data to download; current or obsolete [Default: current] 28 | ## current => /pub/pdb/data/structures/divided 29 | ## obsolete => /pub/pdb/data/structures/obsolete 30 | ## see https://www.rcsb.org/docs/programmatic-access/file-download-services 31 | OPTIONS 32 | die "\n$USAGE\n" unless @ARGV; 33 | 34 | my $outdir = 'PDB'; 35 | my $data = 'current'; 36 | my $nice; 37 | my $verbose; 38 | GetOptions( 39 | 'o|outdir=s' => \$outdir, 40 | 'n|nice=i' => \$nice, 41 | 'd|data=s' => \$data, 42 | 'v|verbose' => \$verbose 43 | ); 44 | 45 | ## Checking output directory 46 | unless (-d $outdir){ 47 | mkdir($outdir, 0755) or die "Cannot create $outdir: $!\n"; 48 | } 49 | 50 | ## Checking data type 51 | $data = lc($data); 52 | my $type = $data; 53 | if ($data eq 'current'){ $data = 'divided'; } 54 | elsif ($data eq 'obsolete'){ $data = 'obsolete'; } 55 | else { 56 | print "Unrecognized data type. Please use current or obsolete.\n"; 57 | print "Exiting...\n"; 58 | exit; 59 | } 60 | 61 | ## Defining niceness / verbosity 62 | my $prg = ""; 63 | if ($nice){ $prg = "nice -n $nice"; } 64 | 65 | ## Running task with adjusted niceness, if desired 66 | print "Downloading $type RCSB PDB files with rsync:\n\n"; 67 | system ("$prg \\ 68 | rsync \\ 69 | -rlpt \\ 70 | --info=progress2 \\ 71 | -z \\ 72 | --delete \\ 73 | --port=33444 \\ 74 | rsync.rcsb.org::ftp_data/structures/$data/pdb/ \\ 75 | $outdir") == 0 or checksig(); 76 | 77 | ### Subroutine(s) 78 | sub checksig { 79 | 80 | my $exit_value = $?; 81 | my $modulo = $exit_value % 255; 82 | 83 | if ($modulo == 2) { 84 | print "\n\nSIGINT detected: Ctrl+C. Exiting...\n\n"; 85 | exit(1); 86 | } 87 | elsif ($modulo == 131) { 88 | print "\n\nSIGTERM detected: Ctrl+\\. Exiting...\n\n"; 89 | exit(1); 90 | } 91 | 92 | } -------------------------------------------------------------------------------- /Images/Bad_Match.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PombertLab/3DFI/e4e0eb13e01393aa0cc4214b48860e80167a472e/Images/Bad_Match.png -------------------------------------------------------------------------------- /Images/Bad_Predicted_Fold.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PombertLab/3DFI/e4e0eb13e01393aa0cc4214b48860e80167a472e/Images/Bad_Predicted_Fold.png -------------------------------------------------------------------------------- /Images/ECU03_1140-m4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PombertLab/3DFI/e4e0eb13e01393aa0cc4214b48860e80167a472e/Images/ECU03_1140-m4.png 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-------------------------------------------------------------------------------- https://raw.githubusercontent.com/PombertLab/3DFI/e4e0eb13e01393aa0cc4214b48860e80167a472e/Images/bfactor_key_cmd.png -------------------------------------------------------------------------------- /Images/no_homology.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PombertLab/3DFI/e4e0eb13e01393aa0cc4214b48860e80167a472e/Images/no_homology.png -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2020 Pombert Lab 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /Misc_tools/rename_files.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab 2020 3 | my $version = '0.2'; 4 | my $name = 'rename_files.pl'; 5 | my $updated = '2021-03-12'; 6 | 7 | use strict; 8 | use warnings; 9 | use Getopt::Long qw(GetOptions); 10 | 11 | ## Usage definition 12 | my $USAGE = <<"OPTIONS"; 13 | NAME ${name} 14 | VERSION ${version} 15 | UPDATED ${updated} 16 | SYNOPSIS Rename file(s) using regular expressions 17 | 18 | USAGE EXAMPLE ${name} \\ 19 | -o 'i{0,1}-t26_1-p1' \\ 20 | -n '' \\ 21 | -f *.fasta 22 | 23 | OPTIONS: 24 | -o (--old) Old pattern/regular expression to replace with new pattern 25 | -n (--new) New pattern to replace with; defaults to blank [Default: ''] 26 | -f (--files) Files to rename 27 | OPTIONS 28 | die "\n$USAGE\n" unless @ARGV; 29 | 30 | ## Defining options 31 | my $old; 32 | my $new = ''; 33 | my @files; 34 | GetOptions( 35 | 'o|old=s' => \$old, 36 | 'n|new=s' => \$new, 37 | 'f|files=s@{1,}' => \@files 38 | ); 39 | 40 | while (my $file = shift @files){ 41 | my $nfile = $file; 42 | $nfile =~ s/$old/$new/; 43 | print "Renaming $file to $nfile\n"; 44 | system "mv $file $nfile"; 45 | } -------------------------------------------------------------------------------- /Misc_tools/split_PDB.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab 2020 3 | my $version = '0.4'; 4 | my $name = 'split_PDB.pl'; 5 | my $updated = '2022-02-24'; 6 | 7 | use strict; 8 | use warnings; 9 | use PerlIO::gzip; 10 | use File::Basename; 11 | use File::Path qw(make_path); 12 | use Getopt::Long qw(GetOptions); 13 | 14 | ## Usage definition 15 | my $USAGE = <<"OPTIONS"; 16 | NAME ${name} 17 | VERSION ${version} 18 | UPDATED ${updated} 19 | SYNOPSIS Splits a PDB file into separate files, one per chain 20 | 21 | USAGE EXAMPLE ${name} \\ 22 | -p files.pdb \\ 23 | -o output_folder \\ 24 | -e pdb 25 | 26 | OPTIONS: 27 | -p (--pdb) PDB input file (supports gzipped files) 28 | -o (--outdir) Output directory [Default: ./] 29 | -e (--ext) Desired file extension [Default: pdb] 30 | OPTIONS 31 | die "\n$USAGE\n" unless @ARGV; 32 | 33 | ## Defining options 34 | my @pdb; 35 | my $outdir = './'; 36 | my $ext = 'pdb'; 37 | GetOptions( 38 | 'p|pdb=s@{1,}' => \@pdb, 39 | 'o|outdir=s' => \$outdir, 40 | 'e|ext=s' => \$ext 41 | ); 42 | 43 | ## Output dir 44 | unless (-d $outdir) { 45 | make_path( $outdir, { mode => 0755 } ) or die "Can't create $outdir: $!\n"; 46 | } 47 | 48 | ## Working on PDB files 49 | while (my $pdb = shift@pdb){ 50 | 51 | my ($filename, $dir) = fileparse($pdb); 52 | my ($prefix) = $filename =~ /^(\w+)/; 53 | 54 | ## Creating subdir per PDB file 55 | my $subdir = "$outdir/$prefix"; 56 | mkdir ("$subdir",0755) or die "Can't create folder $subdir: $!\n"; 57 | 58 | ## Working on PDB file 59 | my $gzip = ''; 60 | if ($pdb =~ /.gz$/){ $gzip = ':gzip'; } 61 | open PDB, "<$gzip", "$pdb" or die "Can't open PDB file $pdb: $!\n"; 62 | 63 | my @header; 64 | my $chain; 65 | my %chains; 66 | my $type = ''; 67 | 68 | while (my $line = ){ 69 | 70 | chomp $line; 71 | 72 | if ($line =~ /^HEADER|TITLE|SOURCE|KEYWDS|EXPDTA|REVDAT|JRNL/){ 73 | push (@header, $line); 74 | } 75 | ## Check if chain is amino acids 76 | elsif ($line =~ /^ATOM.{13}\w{3}\s(\w)/){ 77 | $type = 'aa'; 78 | $chain = $1; 79 | push (@{$chains{$chain}}, $line); 80 | } 81 | ## Check if chain is nucleotide or something else 82 | elsif ($line =~ /^ATOM/){ 83 | $type = 'unknown'; 84 | $chain = undef; 85 | } 86 | ## Only push if chain is amino acids 87 | elsif ($line =~ /^TER/){ 88 | if ($type eq 'aa'){ 89 | if (defined $chain){ 90 | push (@{$chains{$chain}}, $line); 91 | } 92 | else { 93 | print STDERR "File $pdb: $line\n"; 94 | } 95 | } 96 | } 97 | 98 | } 99 | if ($gzip eq ':gzip'){ binmode PDB, ":gzip(none)"; } 100 | 101 | ## Working on chains 102 | for my $ch (keys %chains){ 103 | 104 | open OUT, ">", "$subdir/${prefix}_$ch.$ext" or die "Can't create PDB file $pdb in folder $subdir: $!\n"; 105 | 106 | ## write header 107 | foreach (@header){ 108 | print OUT "$_\n"; 109 | } 110 | my @core = @{$chains{$ch}}; 111 | for (0..$#core){ 112 | print OUT "$core[$_]\n"; 113 | } 114 | 115 | close OUT; 116 | } 117 | } -------------------------------------------------------------------------------- /Notes/Installation_notes.sh: -------------------------------------------------------------------------------- 1 | ## On Fedora 34 2 | ##### Installing Aria2, Conda and Docker ##### 3 | sudo dnf install aria2 conda docker 4 | sudo dnf install python-docker 5 | sudo dnf install python-absl ## absl is required for alphafold 6 | 7 | ## Starting Docker / enabling at boot 8 | sudo systemctl start docker 9 | sudo systemctl enable docker.service 10 | sudo systemctl enable containerd.service 11 | 12 | ## Testing docker 13 | sudo docker run hello-world 14 | 15 | ## Creating docker group + add user(s) to it + activate docker group changes 16 | sudo groupadd docker 17 | sudo usermod -aG docker $USER 18 | newgrp docker 19 | 20 | ## Installing NVIDIA docker container 21 | # On Fedora 34 (https://www.if-not-true-then-false.com/2020/install-nvidia-container-toolkit-on-fedora/) 22 | sudo wget -O /etc/yum.repos.d/inttf.repo https://rpms.if-not-true-then-false.com/inttf.repo 23 | sudo dnf install nvidia-docker2 24 | 25 | # On Fedora 35 (https://blog.shawonashraf.com/nvidia-podman-fedora-34) 26 | ## Alphafold2 expects nvidia-docker2, which is becoming obsolete... 27 | ## Workaround with the newer nvidia-container-runtime 28 | distribution=rhel8.3 29 | curl -s -L https://nvidia.github.io/nvidia-container-runtime/$distribution/nvidia-container-runtime.repo | \ 30 | sudo tee /etc/yum.repos.d/nvidia-container-runtime.repo 31 | sudo dnf install nvidia-container-runtime 32 | 33 | sudo nano /etc/docker/daemon.json 34 | ## Content of .json configuration file, link nvidia to proper path 35 | { 36 | "runtimes": { 37 | "nvidia": { 38 | "path": "/usr/bin/nvidia-container-runtime", 39 | "runtimeArgs": [] 40 | } 41 | } 42 | } 43 | ## EOF 44 | sudo systemctl daemon-reload 45 | sudo systemctl restart docker 46 | 47 | 48 | ## Modifying configuration file 49 | sudo nano /etc/nvidia-container-runtime/config.toml 50 | # Remove comment from 'no-cgroups = false' and change to 'no-cgroups = true' 51 | # Under [nvidia-container-runtime] 52 | # Remove comment (enable): debug = "/var/log/nvidia-container-runtime.log" 53 | 54 | ## Restarting Docker and checking that nvidia configuration is working 55 | systemctl restart docker 56 | nvidia-container-cli info 57 | docker run \ 58 | --privileged \ 59 | --gpus all \ 60 | --rm nvidia/cuda:11.1-base \ 61 | nvidia-smi 62 | 63 | ## Make sure to add --privileged to prevent 'Failed to initialize NVML: Unknown Error' 64 | ## Add user(s) to docker group 65 | 66 | ## Testing capabilities with sample 67 | docker run \ 68 | --privileged \ 69 | --gpus all \ 70 | --rm nvcr.io/nvidia/k8s/cuda-sample:nbody nbody \ 71 | -benchmark \ 72 | -numbodies=512000 73 | -------------------------------------------------------------------------------- /Prediction/AlphaFold2/get_pLDDTs.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab, 2022 3 | my $name = 'get_pLDDTs.pl'; 4 | my $version = '0.1a'; 5 | my $updated = '2022-03-02'; 6 | 7 | use strict; 8 | use warnings; 9 | use File::Basename; 10 | use File::Path qw(make_path); 11 | use Getopt::Long qw(GetOptions); 12 | 13 | my $usage = <<"USAGE"; 14 | NAME ${name} 15 | VERSION ${version} 16 | SYNOPSIS Generates a tab-delimited table of pLDDTs scores for each AlphaFold model 17 | from the ranking_debug.json files. 18 | 19 | COMMAND ${name} -a AlphaFold_results/ -o AlphaFold_summary.tsv 20 | 21 | OPTIONS: 22 | -a (--adir) AlphaFold results directory/directories 23 | -o (--out) Output file 24 | USAGE 25 | die "\n$usage\n" unless @ARGV; 26 | 27 | my @adir; 28 | my $outfile; 29 | GetOptions( 30 | 'a|adir=s@{1,}' => \@adir, 31 | 'o|out=s' => \$outfile 32 | ); 33 | 34 | ## Creating outdir if needed 35 | if ($outfile){ 36 | my ($filename,$path) = fileparse($outfile); 37 | if (defined $path){ 38 | unless(-d $path){ 39 | make_path($path,{mode=>0755}); 40 | } 41 | } 42 | open OUTFILE, ">", $outfile or die "Can't create $outfile: $!\n"; 43 | } 44 | 45 | my %af_results; 46 | 47 | ## Reading AlphaFold directory 48 | while (my $adir = shift@adir){ 49 | opendir (ADIR, $adir) or die "Can't open $adir: $!\n"; 50 | while (my $dname = readdir(ADIR)) { 51 | if (-d "$adir/$dname"){ 52 | unless (($dname eq '.') or ($dname eq '..')){ 53 | ## Checking if .json file is in AlphaFold subdir 54 | my $json = "$adir/$dname/ranking_debug.json"; 55 | if (-e $json){ 56 | open JSON, "<", $json or die "Can't open $json: $!\n"; 57 | my %plDDTs; 58 | my $flag; 59 | my $rank = 0; 60 | while (my $line = ){ 61 | chomp $line; 62 | if ($line =~ /\"(model_\d)\": (.*)/){ 63 | my $model = $1; 64 | my $plDDT = $2; 65 | $plDDT =~ s/,//; 66 | $plDDTs{$model} = $plDDT; 67 | } 68 | elsif ($line =~ /\"order\"\:/){ 69 | $flag = 'order'; 70 | } 71 | elsif ($line =~ /"(model_\d)"/){ 72 | my $model = $1; 73 | if ($flag eq 'order'){ 74 | my $mnum = $rank + 1; 75 | $af_results{$dname}{$mnum}{'3DFI'} = "${dname}-m$mnum.pdb"; 76 | $af_results{$dname}{$mnum}{'plDDT'} = $plDDTs{$model}; 77 | $af_results{$dname}{$mnum}{'ranked'} = "ranked_$rank.pdb"; 78 | $af_results{$dname}{$mnum}{'unranked'} = "unrelaxed_$model.pdb"; 79 | $rank++; 80 | } 81 | } 82 | 83 | } 84 | } 85 | else { 86 | print STDERR "No .json file for $dname in $adir => no ranked models ?!\n"; 87 | } 88 | } 89 | } 90 | } 91 | } 92 | 93 | ## Creating output file 94 | print OUTFILE "### Protein\t3DFI name\tplDDT score\tAlphaFold ranked name\tAlphaFold unranked name\n"; 95 | foreach my $key (sort (keys %af_results)){ 96 | for (1..5){ 97 | print OUTFILE "$key\t"; 98 | print OUTFILE "$af_results{$key}{$_}{'3DFI'}\t"; 99 | print OUTFILE "$af_results{$key}{$_}{'plDDT'}\t"; 100 | print OUTFILE "$af_results{$key}{$_}{'ranked'}\t"; 101 | print OUTFILE "$af_results{$key}{$_}{'unranked'}\n"; 102 | } 103 | } 104 | -------------------------------------------------------------------------------- /Prediction/AlphaFold2/parse_af_results.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert lab, Illinois Tech, 2021 3 | my $name = 'parse_af_results'; 4 | my $version = '0.4'; 5 | my $updated = '2021-09-07'; 6 | 7 | use strict; 8 | use warnings; 9 | use Getopt::Long qw(GetOptions); 10 | 11 | my $usage =<<"OPTIONS"; 12 | NAME ${name} 13 | VERSION ${version} 14 | UDPATED ${updated} 15 | SYNOPSIS Parses the AlphaFold results and rename the outputs with the protein names. 16 | 17 | EXAMPLE ${name} \\ 18 | -a AlphaFold2_results/ \\ 19 | -o Parsed_results \\ 20 | -p k \\ 21 | -t 1 \\ 22 | -s 23 | 24 | OPTIONS: 25 | -a (--afdir) AlphaFold output directory 26 | -o (--outdir) Parsed output directory 27 | -p (--pdbtype) ranked (k), relaxed (r), unrelaxed (u), all (a) [Default: k] 28 | -t (--top) Top X number of pdb files to keep, from best to worst (max 5) [Default: 1] 29 | -s (--standard) Uses standardized model names (-m1 to -m5) instead of -r0 to -r4 for ranked PDB files 30 | -v (--verbose) Adds verbosity 31 | OPTIONS 32 | die "\n$usage\n" unless @ARGV; 33 | 34 | my $afdir; 35 | my $outdir; 36 | my $pdbtype = 'k'; 37 | my $standard; 38 | my $top = 1; 39 | my $verbosity; 40 | GetOptions( 41 | 'a|afdir=s' => \$afdir, 42 | 'o|outdir=s' => \$outdir, 43 | 'p|pdbtype=s' => \$pdbtype, 44 | 's|standard' => \$standard, 45 | 't|top=i' => \$top, 46 | 'v|verbosity' => \$verbosity 47 | ); 48 | 49 | ## Checking number of pdb templates requested 50 | if ($top > 5){ 51 | die "\nPlease enter a number between 1 and 5. AlphaFold2 generates a total of 5 models.\n\n"; 52 | } 53 | 54 | ## Setting to lowercase to prevent possible typos 55 | $pdbtype = lc($pdbtype); 56 | 57 | ## Check output directory 58 | unless (-d $outdir){ mkdir ($outdir, 0755) or die "Can't create $outdir: $!\n" ; } 59 | 60 | ## Parsing files 61 | opendir (DIR, $afdir) or die "Can't open AlphaFold2 folder $afdir: $!\n"; 62 | my @results; 63 | if ($verbosity) { print "\n"; } 64 | while (my $subfolder = readdir(DIR)) { 65 | if (-d "$afdir/$subfolder"){ 66 | unless ( ($subfolder eq '.') or ($subfolder eq '..') ){ 67 | if ($verbosity) { print "Found subfolder: $subfolder\n"; } 68 | push (@results, $subfolder); 69 | } 70 | } 71 | } 72 | if ($verbosity) { print "\n"; } 73 | 74 | my $result; 75 | while ($result = shift @results){ 76 | 77 | ## Ranked models 78 | if (($pdbtype eq 'k') or ($pdbtype eq 'ranked')){ pdb_out('ranked', 'k', 1); } 79 | 80 | ## Relaxed models 81 | elsif (($pdbtype eq 'r') or ($pdbtype eq 'relaxed')){ pdb_out('relaxed_model', 'r', 0); } 82 | 83 | ## Unrelaxed models 84 | elsif (($pdbtype eq 'u') or ($pdbtype eq 'unrelaxed')){ pdb_out('unrelaxed_model', 'u', 0); } 85 | 86 | ## All models 87 | elsif (($pdbtype eq 'a') or ($pdbtype eq 'all')){ 88 | pdb_out('ranked', 'k', 1); ## Ranked 89 | pdb_out('relaxed_model', 'r', 0); ## Relaxed 90 | pdb_out('unrelaxed_model', 'u', 0); ## Unrelaxed 91 | } 92 | 93 | ## If unrecognized command line: 94 | else { die "\nUnrecognized pdbtype: please enter ranked (k), relaxed (r), unrelaxed (u), or all (a)\n\n"; } 95 | 96 | } 97 | 98 | ### Subroutine 99 | sub pdb_out { 100 | 101 | my ($model_name, $moniker, $phase) = @_; 102 | 103 | for my $num (1-$phase..$top-$phase){ 104 | 105 | ## Original PDB name in AlphaFold folder 106 | my $original_pdb = "$afdir/$result/${model_name}_$num.pdb"; 107 | 108 | ## Checking for standardization flag for ranked files 109 | unless (($moniker eq 'r') or ($moniker eq 'u')){ 110 | if ($standard){ 111 | $num++; 112 | $moniker = 'm'; 113 | } 114 | } 115 | 116 | ## Output file name 117 | my $out_pdb = "$outdir/$result-${moniker}${num}.pdb"; 118 | if (-f $original_pdb){ 119 | unless (-f $out_pdb){ system "cp $original_pdb $out_pdb"; } 120 | } 121 | else { 122 | print STDERR "Error: $original_pdb not found. Check if folding of $result completed correctly.\n"; 123 | } 124 | 125 | if ($verbosity){ 126 | print "Copying $original_pdb => $out_pdb\n"; 127 | } 128 | 129 | } 130 | } -------------------------------------------------------------------------------- /Prediction/RoseTTAFold/install_pyrosetta.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | set -e ## exit if a command exits with a non-zero status. 4 | 5 | # >>> conda initialize >>> 6 | __conda_setup="$('conda' 'shell.bash' 'hook' 2> /dev/null)" 7 | eval "$__conda_setup" 8 | unset __conda_setup 9 | # <<< conda initialize <<< 10 | 11 | ## Download - https://www.pyrosetta.org/downloads#h.xe4c0yjfkl19 12 | ## License - https://els2.comotion.uw.edu/product/pyrosetta 13 | PYROSETTA="$1" # Pyrosetta [Python-3.7.Release] 14 | TMPDIR=`realpath -s $2` # tmp_dir 15 | CWDDIR=`pwd` 16 | 17 | ## Activating the folding environment for RoseTTAFold 18 | conda activate folding 19 | 20 | mkdir -p $TMPDIR 21 | tar -xjvf $PYROSETTA -C $TMPDIR 22 | cd $TMPDIR/PyRosetta4.* 23 | cd setup && python setup.py install 24 | cd $CWDDIR 25 | rm -R $TMPDIR 26 | 27 | conda deactivate -------------------------------------------------------------------------------- /Prediction/RoseTTAFold/parse_rf_results.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert lab, Illinois Tech, 2021 3 | my $name = 'parse_rf_results'; 4 | my $version = '0.2a'; 5 | my $updated = '2021-09-07'; 6 | 7 | use strict; 8 | use warnings; 9 | use Getopt::Long qw(GetOptions); 10 | 11 | my $usage =<<"OPTIONS"; 12 | NAME ${name} 13 | VERSION ${version} 14 | UDPATED ${updated} 15 | SYNOPSIS Parses the RoseTTAFold results and rename the outputs with the protein names. 16 | 17 | EXAMPLE ${name} \\ 18 | -a RoseTTAFold_results/ \\ 19 | -o Parsed_results \\ 20 | -p e2e \\ 21 | -t 1 22 | 23 | OPTIONS: 24 | -r (--rfdir) RoseTTAFold output directory 25 | -o (--outdir) Parsed output directory 26 | -p (--pdbtype) PDB type: pyrosetta (py) or end-to-end (e2e) [Default: e2e] 27 | -t (--top) Top X number of pdb files to keep for pyrosetta PDBs, from best to worst (max 5) [Default: 1] 28 | -v (--verbose) Adds verbosity 29 | OPTIONS 30 | die "\n$usage\n" unless @ARGV; 31 | 32 | my $rfdir; 33 | my $outdir; 34 | my $pdbtype = 'e2e'; 35 | my $top = 1; 36 | my $verbosity; 37 | GetOptions( 38 | 'r|rfdir=s' => \$rfdir, 39 | 'o|outdir=s' => \$outdir, 40 | 'p|pdbtype=s' => \$pdbtype, 41 | 't|top=i' => \$top, 42 | 'v|verbosity' => \$verbosity 43 | ); 44 | 45 | ## Checking number of pdb templates requested 46 | if ($top > 5){ 47 | die "\nPlease enter a number between 1 and 5. RoseTTAFold generates a total of 5 models.\n\n"; 48 | } 49 | 50 | ## Setting to lowercase to prevent possible typos 51 | $pdbtype = lc($pdbtype); 52 | 53 | ## Check output directory 54 | unless (-d $outdir){ mkdir ($outdir, 0755) or die "Can't create $outdir: $!\n" ; } 55 | 56 | ## Parsing files 57 | opendir (DIR, $rfdir) or die "Can't open RoseTTAFold folder $rfdir: $!\n"; 58 | my @results; 59 | if ($verbosity) { print "\n"; } 60 | while (my $subfolder = readdir(DIR)) { 61 | if (-d "$rfdir/$subfolder"){ 62 | unless ( ($subfolder eq '.') or ($subfolder eq '..') ){ 63 | if ($verbosity) { print "Found subfolder: $subfolder\n"; } 64 | push (@results, $subfolder); 65 | } 66 | } 67 | } 68 | if ($verbosity) { print "\n"; } 69 | 70 | while (my $result = shift @results){ 71 | 72 | ## e2e 73 | if (($pdbtype eq 'e2e') or ($pdbtype eq 'end-to-end')){ 74 | 75 | my $filename = "$rfdir/$result/t000_.e2e.pdb"; 76 | my $outfile = "$outdir/$result-m1.pdb"; 77 | 78 | if (-f "$filename"){ 79 | unless (-f $outfile) { system "cp $filename $outfile"; } 80 | } 81 | else { 82 | print "$result: No PDB file found. "; 83 | print "Check for possible video RAM issue ('RuntimeError: CUDA out of memory') in $rfdir/$result/log/network.stderr.\n"; 84 | } 85 | } 86 | ## pyrosetta 87 | elsif (($pdbtype eq 'py') or ($pdbtype eq 'pyrosetta')){ 88 | for my $num (1..$top){ 89 | 90 | my $filename = "$rfdir/$result/model/model_$num.crderr.pdb"; 91 | my $outfile = "$outdir/$result-m$num.pdb"; 92 | 93 | unless (-f $outfile) { system "cp $filename $outfile"; } 94 | } 95 | } 96 | ## If unrecognized command line: 97 | else { die "\nUnrecognized pdbtype: please enter end-to-end (e2e) or pyrosetta (py).\n\n"; } 98 | 99 | } -------------------------------------------------------------------------------- /Prediction/RoseTTAFold/rosettafold.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab, Illinois Tech, 2021 3 | my $name = 'rosettafold.pl'; 4 | my $version = '0.1'; 5 | my $updated = '2021-07-22'; 6 | 7 | use strict; 8 | use warnings; 9 | use Getopt::Long qw(GetOptions); 10 | use File::Basename; 11 | 12 | my $usage = <<"OPTIONS"; 13 | NAME ${name} 14 | VERSION ${version} 15 | UPDATED ${updated} 16 | SYNOPSIS Runs RoseTTAFold from in batch mode 17 | 18 | REQUIREMENTS RoseTTAFold - https://github.com/RosettaCommons/RoseTTAFold 19 | PyRosetta - https://www.pyrosetta.org/ 20 | Conda - https://docs.conda.io/en/latest/ 21 | 22 | EXAMPLE ${name} \\ 23 | -f *.fasta \\ 24 | -o RFOLD_3D/ \\ 25 | -t py 26 | 27 | OPTIONS: 28 | -f (--fasta) FASTA files to fold 29 | -o (--outdir) Output directory 30 | -t (--type) Folding type: pyrosetta (py) or end-to-end (e2e) [Default: e2e] 31 | -r (--rosetta) RoseTTAFold installation directory 32 | 33 | NOTES: 34 | - The e2e option requires a GPU with > 8 Gb RAM to tackle larger proteins; pyrosetta is slower but not video RAM constrained 35 | - The -r option is not required if the environment variable \$ROSETTAFOLD_HOME is set, e.g.: 36 | export ROSETTAFOLD_HOME=/opt/RoseTTAFold 37 | OPTIONS 38 | die "\n$usage\n" unless @ARGV; 39 | my @command = @ARGV; 40 | 41 | my @fasta; 42 | my $outdir; 43 | my $folding_type = 'e2e'; 44 | my $rosetta_home; 45 | GetOptions( 46 | 'f|fasta=s@{1,}' => \@fasta, 47 | 'o|outdir=s' => \$outdir, 48 | 't|type=s' => \$folding_type, 49 | 'r|rosetta=s' => \$rosetta_home, 50 | ); 51 | 52 | $folding_type = lc($folding_type); 53 | 54 | ### Checking for RoseTTAFold installation; environment variables in Perl are loaded in %ENV 55 | # Checking installation folder 56 | if (!defined $rosetta_home){ 57 | if (exists $ENV{'ROSETTAFOLD_HOME'}){ $rosetta_home = $ENV{'ROSETTAFOLD_HOME'}; } 58 | else { 59 | print "WARNING: The RoseTTAFold installation directory is not set as an environment variable (\$ROSETTAFOLD_HOME) and the -r option was not entered.\n"; 60 | print "Please check if RoseTTAFold was installed properly\n\n"; 61 | exit; 62 | } 63 | } 64 | elsif (defined $rosetta_home){ 65 | unless (-d $rosetta_home){ die "WARNING: Can't find RoseTTAFold installation folder: $rosetta_home. Please check command line\n\n"; } 66 | } 67 | 68 | ## Check output directory + creating log file 69 | unless (-d $outdir){ mkdir ($outdir, 0755) or die "Can't create $outdir: $!\n"; } 70 | open LOG, ">>", "$outdir/rosettafold.log" or die "Can't create $outdir/rosettafold.log: $!\n";; 71 | 72 | my $timestamp = localtime; 73 | print LOG "\nCOMMAND = $name @command\n"; 74 | print LOG "\nFolding started on $timestamp\n"; 75 | 76 | ## Running RoseTTAFold on FASTA files 77 | while (my $fasta = shift@fasta){ 78 | 79 | my $basename = fileparse($fasta); 80 | my ($prefix) = $basename =~ /^(.*)\.\w+$/; 81 | 82 | ## Checking if protein structures are already present in output dir 83 | if (-f "$outdir/$prefix/t000_.e2e.pdb"){ 84 | print "\nPDB output found for $basename. Skipping folding...\n"; 85 | next; 86 | } 87 | 88 | else { 89 | my $time = localtime; 90 | print "\n$time: Working on $fasta...\n"; 91 | my $start = time; 92 | 93 | if (($folding_type eq 'py') or ($folding_type eq 'pyrosetta')){ 94 | system ("$rosetta_home/run_pyrosetta_ver.sh \\ 95 | $fasta \\ 96 | $outdir/$prefix") == 0 or checksig(); 97 | } 98 | elsif (($folding_type eq 'e2e') or ($folding_type eq 'end-to-end')){ 99 | system ("$rosetta_home/run_e2e_ver.sh \\ 100 | $fasta \\ 101 | $outdir/$prefix") == 0 or checksig(); 102 | } 103 | else { 104 | die "\nUnrecognized folding type: $folding_type. Please check command line.\n\n"; 105 | } 106 | 107 | my $run_time = time - $start; 108 | $run_time = $run_time/60; 109 | $run_time = sprintf ("%.2f", $run_time); 110 | print "\nTime to fold $basename: $run_time minutes\n"; 111 | print LOG "Time to fold $basename: $run_time minutes\n"; 112 | } 113 | } 114 | 115 | ### Subroutine(s) 116 | sub checksig { 117 | 118 | my $exit_code = $?; 119 | my $modulo = $exit_code % 255; 120 | 121 | print "\nExit code = $exit_code; modulo = $modulo \n"; 122 | 123 | if ($modulo == 2) { 124 | print "\nSIGINT detected: Ctrl+C => exiting...\n"; 125 | exit(2); 126 | } 127 | elsif ($modulo == 131) { 128 | print "\nSIGTERM detected: Ctrl+\\ => exiting...\n"; 129 | exit(131); 130 | } 131 | 132 | } -------------------------------------------------------------------------------- /Prediction/trRosetta/create_npz.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab 2020 3 | my $version = '0.2'; 4 | my $name = 'create_npz.pl'; 5 | my $updated = '2021-07-23'; 6 | 7 | use strict; 8 | use warnings; 9 | use Getopt::Long qw(GetOptions); 10 | use File::Basename; 11 | 12 | ## Usage definition 13 | my $USAGE = <<"OPTIONS"; 14 | NAME ${name} 15 | VERSION ${version} 16 | UPDATED ${updated} 17 | SYNOPSIS Creates .npz files with trRosetta from .a3m files created by hhblits 18 | REQUIREMENTS trRosetta - https://github.com/gjoni/trRosetta 19 | tensorflow 1.15 - https://www.tensorflow.org/ 20 | 21 | NOTES Probably best to run in a conda environment... 22 | NOTES Can quickly eat through 8 Gb of VRAM with large a3m files... 23 | NOTES If so, instead try with: pip install tensorflow-cpu==1.15 24 | 25 | COMMAND ${name} \\ 26 | -a HHBLITS/*.a3m \\ 27 | -o NPZ/ \\ 28 | -t /media/Data_3/opt/trRosetta 29 | 30 | OPTIONS: 31 | -a (--a3m) .a3m files generated by hhblits 32 | -o (--output) Output folder [Default: ./] 33 | -t (--trrosetta) trRosetta installation directory (TRROSETTA_HOME) 34 | -m (--model) trRosetta model directory [Default: model2019_07] 35 | 36 | NOTE: The -t option is not required if the environment variable TRROSETTA_HOME is set, e.g.: 37 | export TRROSETTA_HOME=/opt/tRosetta 38 | OPTIONS 39 | die "\n$USAGE\n" unless @ARGV; 40 | 41 | ## Defining options 42 | my @a3m; 43 | my $out = './'; 44 | my $trrosetta_home; 45 | my $model = 'model2019_07'; 46 | GetOptions( 47 | 'a|a3m=s@{1,}' => \@a3m, 48 | 'o|output=s' => \$out, 49 | 't|trrosetta=s' => \$trrosetta_home, 50 | 'm|model=s' => \$model 51 | ); 52 | 53 | ### Checking for tRosetta installation; environment variables in Perl are loaded in %ENV 54 | # Checking installation folder 55 | if (!defined $trrosetta_home){ 56 | if (exists $ENV{'TRROSETTA_HOME'}){ $trrosetta_home = $ENV{'TRROSETTA_HOME'}; } 57 | else { 58 | print "WARNING: The trRosetta installation directory is not set as an environment variable (\$TRROSETTA_HOME) and the -r option was not entered.\n"; 59 | print "Please check if trRosetta was installed properly\n\n"; 60 | exit; 61 | } 62 | } 63 | elsif (defined $trrosetta_home){ 64 | unless (-d $trrosetta_home){ die "WARNING: Can't find trRosetta installation folder: $trrosetta_home. Please check command line\n\n"; } 65 | } 66 | 67 | ## Working on a3m files 68 | unless (-d $out){ 69 | mkdir ($out,0755) or die "Can't create folder $out: $!\n"; 70 | } 71 | 72 | while (my $a3m = shift@a3m){ 73 | 74 | my($name, $dir) = fileparse($a3m); 75 | my ($prefix) = $name =~ /^(\S+)\.(\w+)$/; 76 | 77 | print "\nWorking on file: $name\n\n"; 78 | 79 | system "python \\ 80 | $trrosetta_home/network/predict.py \\ 81 | -m $trrosetta_home/$model \\ 82 | $a3m \\ 83 | $out/$prefix.npz"; 84 | } -------------------------------------------------------------------------------- /Prediction/trRosetta/fasta_oneliner.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab 2020 3 | my $version = '0.2a'; 4 | my $name = 'fasta_oneliner.pl'; 5 | my $updated = '2021-04-21'; 6 | 7 | use strict; 8 | use warnings; 9 | use Getopt::Long qw(GetOptions); 10 | use File::Basename; 11 | 12 | ## Usage definition 13 | my $USAGE = <<"OPTIONS"; 14 | NAME ${name} 15 | VERSION ${version} 16 | UPDATED ${updated} 17 | SYNOPSIS Convert FASTA sequences into single string FASTA 18 | 19 | COMMAND ${name} \\ 20 | -f *.fasta \\ 21 | -o FASTA_OL 22 | 23 | OPTIONS: 24 | -f (--fasta) FASTA files to convert 25 | -o (--output) Output folder [Default = FASTA_OL] 26 | OPTIONS 27 | die "\n$USAGE\n" unless @ARGV; 28 | 29 | ## Defining options 30 | my @fasta; 31 | my $out = "FASTA_OL"; 32 | GetOptions( 33 | 'f|fasta=s@{1,}' => \@fasta, 34 | 'o|output=s' => \$out, 35 | ); 36 | 37 | ## Checking output directory 38 | unless (-d $out){ 39 | mkdir ($out,0755) or die "Can't create folder $out: $!\n"; 40 | } 41 | 42 | ## Converting fasta files 43 | while (my $fasta = shift@fasta){ 44 | 45 | open FASTA, "<", "$fasta" or die "Can't open $fasta: $!\n"; 46 | my($name, $dir) = fileparse($fasta); 47 | my $header; 48 | my $seq; 49 | 50 | while (my $line = ){ 51 | chomp $line; 52 | if ($line =~ /^>/){ $header = $line; } 53 | else{ $seq .= $line; } 54 | } 55 | 56 | open OUT, ">", "$out/$name" or die "Can't create $out/$name: $!\n";; 57 | print OUT "$header\n"."$seq\n"; 58 | close FASTA; 59 | close OUT; 60 | } -------------------------------------------------------------------------------- /Prediction/trRosetta/run_hhblits.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab 2020 3 | my $version = '0.2c'; 4 | my $name = 'run_hhblits.pl'; 5 | my $updated = '2021-04-21'; 6 | 7 | use strict; 8 | use warnings; 9 | use Getopt::Long qw(GetOptions); 10 | 11 | my @command = @ARGV; ## Keeping track of command line for log 12 | 13 | ## Usage definition 14 | my $USAGE = <<"OPTIONS"; 15 | NAME ${name} 16 | VERSION ${version} 17 | UPDATED ${updated} 18 | SYNOPSIS Runs hhblits on provided fasta files to create .a3m files 19 | REQUIREMENTS HH-suite3 - https://github.com/soedinglab/hh-suite 20 | UNICLUST database - https://uniclust.mmseqs.com/ 21 | 22 | COMMAND ${name} \\ 23 | -t 10 \\ 24 | -f FASTA_OL/ \\ 25 | -o HHBLITS/ \\ 26 | -d /media/Data_3/Uniclust/UniRef30_2020_06 \\ 27 | -e 1e-40 1e-10 1e-03 28 | 29 | OPTIONS: 30 | -t (--threads) Number of threads to use [Default: 10] 31 | -f (--fasta) Folder containing fasta files 32 | -o (--output) Output folder [Default: ./] 33 | -d (--database) Uniclust database to query 34 | -v (--verbosity) hhblits verbosity; 0, 1 or 2 [Default: 2] 35 | 36 | ## E-value options 37 | -e (--evalues) Desired evalue(s) to query independently 38 | -s (--seq_it) Iterates sequentially through evalues 39 | -se (--seq_ev) Evalues to iterate through sequentially [Default: 40 | 1e-70 1e-60 1e-50 1e-40 1e-30 1e-20 1e-10 1e-08 1e-06 1e-04 1e+01 ] 41 | -ne (--num_it) # of hhblits iteration per evalue (-e) [Default: 3] 42 | -ns (--num_sq) # of hhblits iteration per sequential evalue (-s) [Default: 1] 43 | OPTIONS 44 | die "\n$USAGE\n" unless @ARGV; 45 | 46 | ## Defining options 47 | my $threads = 10; 48 | my $dir; 49 | my $out = './'; 50 | my $uniclust; 51 | my $verb = 2; 52 | my @evalues; 53 | my $sqit; 54 | my @seqev; 55 | my $nint = 3; 56 | my $nseq = 1; 57 | GetOptions( 58 | 't|threads=i' => \$threads, 59 | 'f|fasta=s' => \$dir, 60 | 'o|output=s' => \$out, 61 | 'd|database=s' => \$uniclust, 62 | 'v|verbosity=i' => \$verb, 63 | 'e|evalues=s@{1,}' => \@evalues, 64 | 's|seq_it' => \$sqit, 65 | 'se|seq_ev=s@{1,}' => \@seqev, 66 | 'ne|num_it=i' => \$nint, 67 | 'ns|num_sq=i' => \$nseq 68 | ); 69 | 70 | ## Reading from folder 71 | unless (-d $out){mkdir ($out,0755) or die "Can't create folder $out: $!\n";} 72 | opendir (DIR, $dir) or die $!; 73 | my @fasta; 74 | while (my $fasta = readdir(DIR)){ 75 | if (($fasta eq '.') || ($fasta eq '..')){next;} 76 | elsif ($fasta =~ /.hhr$/){next;} ## Skipping previous hhblits results, if any 77 | else{push (@fasta, $fasta);} 78 | } 79 | @fasta = sort@fasta; 80 | 81 | ## Running hhblits 82 | my $start = localtime(); 83 | open LOG, ">", "$out/hhblits.log"; 84 | print LOG "COMMAND LINE:\n$name @command\n"."$name version = $version\n"; 85 | print LOG "hhblits search(es) started on: $start\n"; 86 | while (my $fasta = shift@fasta){ 87 | my ($prefix, $ext) = $fasta =~ /^(\S+)\.(\w+)$/; 88 | ## Running independent searches per evalue 89 | if (@evalues){ 90 | foreach my $eval (@evalues){ 91 | print "\nWorking on file $dir/$fasta with evalue $eval ...\n\n"; 92 | system "hhblits \\ 93 | -cpu $threads \\ 94 | -i $dir/$fasta \\ 95 | -oa3m $out/$prefix.$eval.a3m \\ 96 | -d $uniclust \\ 97 | -e $eval \\ 98 | -n $nint \\ 99 | -v $verb"; 100 | } 101 | } 102 | ## Running iterative searches, from stricter to more permissive evalues 103 | if ($sqit){ 104 | 105 | my $filename = "$out/$prefix.sqit.a3m"; 106 | my @seqit = (1e-70, 1e-60, 1e-50, 1e-40, 1e-30, 1e-20, 1e-10, 1e-08, 1e-06, 1e-04, 1e+01); 107 | if (@seqev){@seqit = @seqev;} 108 | my $start = shift@seqit; 109 | 110 | if(-f $filename){ 111 | print "File $filename exists, skipping...\n"; 112 | next; 113 | } 114 | 115 | print "\nIterating on file $dir/$fasta with evalue $start ...\n\n"; 116 | system "hhblits \\ 117 | -cpu $threads \\ 118 | -i $dir/$fasta \\ 119 | -oa3m $filename \\ 120 | -d $uniclust \\ 121 | -e $start \\ 122 | -n $nseq \\ 123 | -v $verb"; 124 | 125 | foreach my $eval (@seqit){ 126 | print "\nIterating on file $dir/$fasta with evalue $eval ...\n\n"; 127 | system "hhblits \\ 128 | -cpu $threads \\ 129 | -i $filename \\ 130 | -oa3m $filename \\ 131 | -d $uniclust \\ 132 | -e $eval \\ 133 | -n $nseq \\ 134 | -v $verb"; 135 | } 136 | } 137 | } 138 | my $mend = localtime(); 139 | print LOG "hhblits search(es) completed on $mend\n\n"; 140 | -------------------------------------------------------------------------------- /Prediction/trRosetta/sanitize_pdb.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab 2020 3 | my $version = '0.2a'; 4 | my $name = 'sanitize_pdb.pl'; 5 | my $updated = '2021-04-21'; 6 | 7 | use strict; 8 | use warnings; 9 | use Getopt::Long qw(GetOptions); 10 | use File::Basename; 11 | 12 | ## Usage definition 13 | my $USAGE = <<"OPTIONS"; 14 | NAME ${name} 15 | VERSION ${version} 16 | UPDATED ${updated} 17 | SYNOPSIS Cleans .pdb files genrated with trRosetta to remove non-standard PDB entries 18 | 19 | COMMAND ${name} \\ 20 | -p PDB/*.pdb \\ 21 | -o PDB_clean 22 | 23 | OPTIONS: 24 | -p (--pdb) .pdb files generated by trRosetta 25 | -o (--output) Output folder [Default: ./] 26 | OPTIONS 27 | die "\n$USAGE\n" unless @ARGV; 28 | 29 | ## Defining options 30 | my @pdb; 31 | my $out = './'; 32 | GetOptions( 33 | 'p|pdb=s@{1,}' => \@pdb, 34 | 'o|output=s' => \$out, 35 | ); 36 | 37 | ## Checking output directory 38 | unless (-d $out){ 39 | mkdir ($out,0755) or die "Can't create folder $out: $!\n"; 40 | } 41 | 42 | ## cleaning up pdb files 43 | while (my $pdb = shift@pdb){ 44 | 45 | open PDB, "<", "$pdb" or die "Can't read file $pdb: $!\n"; 46 | my($name, $dir) = fileparse($pdb); 47 | open CLEAN, ">", "$out/$name" or die "Can't create file $out/$name: $!\n"; 48 | 49 | my @tags = ('HEADER', 'EXPDTA', 'REMARK', 'ATOM', 'TER'); 50 | while (my $line = ){ 51 | chomp $line; 52 | foreach (@tags){ 53 | if ($line =~ /^$_/){ print CLEAN "$line\n"; } 54 | } 55 | } 56 | close PDB; 57 | close CLEAN; 58 | } -------------------------------------------------------------------------------- /Prediction/trRosetta/trRosetta_installation_notes.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/bash 2 | 3 | ## On Fedora 34 4 | sudo dnf install aria2 perl-App-cpanminus 5 | 6 | ## Installing HH-suite with AVX2 - https://github.com/soedinglab/hh-suite 7 | HHSUITE=/opt/hhsuite 8 | mkdir -p $HHSUITE 9 | cd $HHSUITE 10 | aria2c -x10 https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz 11 | tar xvfz hhsuite-3.3.0-AVX2-Linux.tar.gz 12 | rm hhsuite-3.3.0-AVX2-Linux.tar.gz 13 | echo "export PATH=$PATH:$(pwd)/bin:$(pwd)/scripts" >> ~/.bashrc 14 | 15 | ## Downloading trRosetta from GitHub: 16 | git clone https://github.com/gjoni/trRosetta 17 | cd trRosetta 18 | 19 | ## Setting up trRosetta installation directory: 20 | echo "export TRROSETTA_HOME=$(pwd)" >> ~/.bashrc 21 | 22 | ## Downloading trRosetta pre-trained network: 23 | aria2c -x10 https://files.ipd.uw.edu/pub/trRosetta/model2019_07.tar.bz2 24 | tar -xvf model2019_07.tar.bz2 25 | 26 | ## Must also download trRosetta structure modeling scripts manually - trRosetta package (28M). 27 | firefox https://yanglab.nankai.edu.cn/trRosetta/download/ 28 | cd ~/Downloads/ 29 | tar -xvf trRosetta.tar.bz2 30 | mv trRosetta $TRROSETTA_HOME/trRosetta_scripts 31 | echo "export TRROSETTA_SCRIPTS=$TRROSETTA_HOME/trRosetta_scripts" >> ~/.bashrc 32 | 33 | ## To install tensorflow with GPU in conda: 34 | ## The files can eat through GPU VRAM very quickly. 8 Gb is usually insufficient... 35 | # conda create -n tfgpu python=3.7 36 | # conda activate tfgpu 37 | # pip install tensorflow-gpu==1.15 38 | # pip install numpy==1.19.5 39 | # conda install cudatoolkit==10.0.130 40 | # conda install cudnn==7.6.5 41 | 42 | ## To install tensorflow with CPU in conda: 43 | conda create -n tfcpu python=3.7 44 | conda activate tfcpu 45 | pip install tensorflow-cpu==1.15 46 | pip install numpy==1.19.5 47 | 48 | ## Installing PyRosetta [Python-3.7.Release] inside conda 49 | ## Goto https://www.pyrosetta.org/downloads to download/request a license 50 | ## See https://www.pyrosetta.org/downloads#h.abjy686qantw for detailed instructions 51 | tar -xvf `ls PyRosetta4.Release.python37*` 52 | cd PyRosetta4.Release.python37.linux.release-289/ 53 | cd setup && python setup.py install 54 | cd ../../ 55 | 56 | ## To test PyRosetta installation 57 | ## python 58 | ## import pyrosetta; pyrosetta.init() 59 | ## quit() 60 | 61 | ## Removing PyRosetta installation files 62 | rm -R PyRosetta4.Release.python37* 63 | 64 | 65 | 66 | -------------------------------------------------------------------------------- /Prediction/trRosetta2/fasta_oneliner.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab 2020 3 | my $version = '0.2a'; 4 | my $name = 'fasta_oneliner.pl'; 5 | my $updated = '2021-04-21'; 6 | 7 | use strict; 8 | use warnings; 9 | use Getopt::Long qw(GetOptions); 10 | use File::Basename; 11 | 12 | ## Usage definition 13 | my $USAGE = <<"OPTIONS"; 14 | NAME ${name} 15 | VERSION ${version} 16 | UPDATED ${updated} 17 | SYNOPSIS Convert FASTA sequences into single string FASTA 18 | 19 | COMMAND ${name} \\ 20 | -f *.fasta \\ 21 | -o FASTA_OL 22 | 23 | OPTIONS: 24 | -f (--fasta) FASTA files to convert 25 | -o (--output) Output folder [Default = FASTA_OL] 26 | OPTIONS 27 | die "\n$USAGE\n" unless @ARGV; 28 | 29 | ## Defining options 30 | my @fasta; 31 | my $out = "FASTA_OL"; 32 | GetOptions( 33 | 'f|fasta=s@{1,}' => \@fasta, 34 | 'o|output=s' => \$out, 35 | ); 36 | 37 | ## Checking output directory 38 | unless (-d $out){ 39 | mkdir ($out,0755) or die "Can't create folder $out: $!\n"; 40 | } 41 | 42 | ## Converting fasta files 43 | while (my $fasta = shift@fasta){ 44 | 45 | open FASTA, "<", "$fasta" or die "Can't open $fasta: $!\n"; 46 | my($name, $dir) = fileparse($fasta); 47 | my $header; 48 | my $seq; 49 | 50 | while (my $line = ){ 51 | chomp $line; 52 | if ($line =~ /^>/){ $header = $line; } 53 | else{ $seq .= $line; } 54 | } 55 | 56 | open OUT, ">", "$out/$name" or die "Can't create $out/$name: $!\n";; 57 | print OUT "$header\n"."$seq\n"; 58 | close FASTA; 59 | close OUT; 60 | } -------------------------------------------------------------------------------- /Prediction/trRosetta2/parse_tr2_results.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert lab, Illinois Tech, 2021 3 | my $name = 'parse_tr2_results'; 4 | my $version = '0.1'; 5 | my $updated = '2021-08-04'; 6 | 7 | use strict; 8 | use warnings; 9 | use Getopt::Long qw(GetOptions); 10 | 11 | my $usage =<<"OPTIONS"; 12 | NAME ${name} 13 | VERSION ${version} 14 | UDPATED ${updated} 15 | SYNOPSIS Parses the trRosetta2 results and rename the outputs with the protein names. 16 | 17 | EXAMPLE ${name} \\ 18 | -r trRosetta2_results/ \\ 19 | -o Parsed_results \\ 20 | -t 1 21 | 22 | OPTIONS: 23 | -r (--r2dir) trRosetta2 output directory 24 | -o (--outdir) Parsed output directory 25 | -t (--top) Top X number of pdb files to keep, from best to worst (max 5) [Default: 1] 26 | -v (--verbose) Adds verbosity 27 | OPTIONS 28 | die "\n$usage\n" unless @ARGV; 29 | 30 | my $r2dir; 31 | my $outdir; 32 | my $top = 1; 33 | my $verbosity; 34 | GetOptions( 35 | 'r|r2dir=s' => \$r2dir, 36 | 'o|outdir=s' => \$outdir, 37 | 't|top=i' => \$top, 38 | 'v|verbosity' => \$verbosity 39 | ); 40 | 41 | ## Checking number of pdb templates requested 42 | if ($top > 5){ 43 | die "\nPlease enter a number between 1 and 5. RoseTTAFold generates a total of 5 models.\n\n"; 44 | } 45 | 46 | ## Parsing files 47 | opendir (DIR, $r2dir) or die "Can't open trRosetta2 folder $r2dir: $!\n"; 48 | my @results; 49 | if ($verbosity) { print "\n"; } 50 | while (my $subfolder = readdir(DIR)) { 51 | if (-d "$r2dir/$subfolder"){ 52 | unless ( ($subfolder eq '.') or ($subfolder eq '..') ){ 53 | if ($verbosity) { print "Found subfolder: $subfolder\n"; } 54 | push (@results, $subfolder); 55 | } 56 | } 57 | } 58 | if ($verbosity) { print "\n"; } 59 | 60 | ## Check output directory 61 | unless (-d $outdir){ mkdir ($outdir, 0755) or die "Can't create $outdir: $!\n" ; } 62 | 63 | while (my $result = shift @results){ 64 | 65 | my $filename = "$r2dir/$result/model/model_1.crderr.pdb"; 66 | 67 | unless (-f $filename){ 68 | print "$result: $filename not found. Check if the folding completed properly\n"; 69 | next; 70 | } 71 | else { 72 | for my $num (1..$top){ 73 | $filename = "$r2dir/$result/model/model_$num.crderr.pdb"; 74 | if (-f $filename) { 75 | system "cp $filename $outdir/$result-m$num.pdb"; 76 | } 77 | } 78 | } 79 | } -------------------------------------------------------------------------------- /Prediction/trRosetta2/trRosetta2.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab, Illinois Tech, 2021 3 | my $name = 'trRosetta2.pl'; 4 | my $version = '0.1'; 5 | my $updated = '2021-08-04'; 6 | 7 | use strict; 8 | use warnings; 9 | use Getopt::Long qw(GetOptions); 10 | use File::Basename; 11 | 12 | my $usage = <<"OPTIONS"; 13 | NAME ${name} 14 | VERSION ${version} 15 | UPDATED ${updated} 16 | SYNOPSIS Runs trRosetta2 from in batch mode 17 | 18 | REQUIREMENTS trRosetta2 - https://github.com/RosettaCommons/trRosetta2 19 | PyRosetta - https://www.pyrosetta.org/ 20 | Conda - https://docs.conda.io/en/latest/ 21 | 22 | EXAMPLE ${name} \\ 23 | -f *.fasta \\ 24 | -o TROS2_3D/ \\ 25 | -g 26 | 27 | OPTIONS: 28 | -f (--fasta) FASTA files to fold 29 | -o (--outdir) Output directory 30 | -g (--gpu) Uses GPU acceleration (>= 16 Gb video RAM recommended); defaults to CPU otherwize 31 | -t (--trrosetta2) trRosetta2 installation directory 32 | 33 | NOTES: 34 | - The -t option is not required if the environment variable \$TRROSETTA2_HOME is set, e.g.: 35 | export TRROSETTA2_HOME=/opt/trRosetta2 36 | OPTIONS 37 | die "\n$usage\n" unless @ARGV; 38 | my @command = @ARGV; 39 | 40 | my @fasta; 41 | my $outdir; 42 | my $gpu; 43 | my $trrosetta2_home; 44 | GetOptions( 45 | 'f|fasta=s@{1,}' => \@fasta, 46 | 'o|outdir=s' => \$outdir, 47 | 'g|gpu' => \$gpu, 48 | 't|trrosetta2=s' => \$trrosetta2_home, 49 | ); 50 | 51 | ### Checking for RoseTTAFold installation; environment variables in Perl are loaded in %ENV 52 | # Checking installation folder 53 | if (!defined $trrosetta2_home){ 54 | if (exists $ENV{'TRROSETTA2_HOME'}){ $trrosetta2_home = $ENV{'TRROSETTA2_HOME'}; } 55 | else { 56 | print "WARNING: The trRosetta2 installation directory is not set as an environment variable (\$TRROSETTA2_HOME) and the -t option was not entered.\n"; 57 | print "Please check if trRosetta2 was installed properly\n\n"; 58 | exit; 59 | } 60 | } 61 | elsif (defined $trrosetta2_home){ 62 | unless (-d $trrosetta2_home){ die "WARNING: Can't find trRosetta2 installation folder: $trrosetta2_home. Please check command line\n\n"; } 63 | } 64 | 65 | ## Check output directory + creating log file 66 | unless (-d $outdir){ mkdir ($outdir, 0755) or die "Can't create $outdir: $!\n"; } 67 | open LOG, ">>", "$outdir/trRosetta2.log" or die "Can't create $outdir/trRosetta2.log: $!\n";; 68 | 69 | my $timestamp = localtime; 70 | print LOG "\nCOMMAND = $name @command\n"; 71 | print LOG "\nFolding started on $timestamp\n"; 72 | 73 | ## Running trRosetta2 on FASTA files 74 | while (my $fasta = shift@fasta){ 75 | 76 | my $basename = fileparse($fasta); 77 | my ($prefix) = $basename =~ /^(.*)\.\w+$/; 78 | 79 | ## Checking if protein structures are already present in output dir 80 | if (-f "$outdir/$prefix/model/model_5.crderr.pdb"){ 81 | print "\nPDB output found for $basename. Skipping folding...\n"; 82 | next; 83 | } 84 | 85 | else { 86 | my $time = localtime; 87 | print "\n$time: Working on $fasta...\n"; 88 | my $start = time; 89 | 90 | ## Running with GPU if flag is on 91 | if ($gpu){ 92 | system "$trrosetta2_home/run_pipeline.sh \\ 93 | $fasta \\ 94 | $outdir/$prefix"; 95 | } 96 | ## Defaulting to cpu otherwise 97 | else { 98 | system "$trrosetta2_home/run_pipeline_cpu.sh \\ 99 | $fasta \\ 100 | $outdir/$prefix"; 101 | } 102 | 103 | my $run_time = time - $start; 104 | $run_time = $run_time/60; 105 | $run_time = sprintf ("%.2f", $run_time); 106 | print "\nTime to fold $basename: $run_time minutes\n"; 107 | print LOG "Time to fold $basename: $run_time minutes\n"; 108 | } 109 | } 110 | -------------------------------------------------------------------------------- /Visualization/Helper_Scripts/chimerax_session_creator.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | from chimerax.core.commands import run 3 | from sys import argv 4 | import argparse 5 | import re 6 | import os 7 | 8 | name = 'chimerax_session_creator.py' 9 | version = '0.3' 10 | updated = '2022-02-23' 11 | 12 | usage = f''' 13 | NAME {name} 14 | VERSION {version} 15 | UPDATED {updated} 16 | 17 | SYNOPSIS This script is used to align a reference .pdb to a predicted .pdb, 18 | changes the predicted .pdb color, hides all atoms, shows only matched 19 | chains, and saves the result as a ChimeraX session, .cxs file. This version 20 | is tested and functional as of ChimeraX 1.3.1. 21 | 22 | COMMAND {name} \\ 23 | -p ...preference \\ 24 | -r ...reference 25 | 26 | OPTIONS 27 | 28 | -p (--pred) Predicted .pdb file 29 | -r (--rcsb) RCSB .pdb file 30 | -m (--match) RCSB match name 31 | -c (--chain) RCSB matched chain 32 | -o (--outdir) Output directory for .cxs files [Default: ./3D_Visualizations] 33 | ''' 34 | 35 | if len(argv) < 2: 36 | print(f"\n\n{usage}\n\n") 37 | exit() 38 | 39 | parser = argparse.ArgumentParser(usage=usage) 40 | parser.add_argument('-p','--pred',type=str,required=True) 41 | parser.add_argument('-r','--rcsb',type=str) 42 | parser.add_argument('-m','--match',type=str,default="NoFileName") 43 | parser.add_argument('-c','--chain',type=str) 44 | parser.add_argument('-o','--outdir',type=str,default="./3D_Visualizations") 45 | parser.add_argument('--nogui') 46 | 47 | args = parser.parse_args() 48 | pred = args.pred 49 | rcsb_match = args.match 50 | rcsb = args.rcsb 51 | rcsb_chain = args.chain 52 | if(args.outdir): 53 | outdir = args.outdir 54 | 55 | locus_tag = os.path.splitext(os.path.basename(pred))[0] 56 | 57 | ## Load pdb files 58 | model_pred = run(session,f"open {pred}")[0] 59 | model_pred_name = (model_pred.id_string) 60 | 61 | model_rcsb = run(session,f"open {rcsb}")[0] 62 | model_rcsb_name = (model_rcsb.id_string) 63 | 64 | 65 | ## Prepare file for display by hiding everything 66 | run(session,"hide atoms") 67 | run(session,"hide ribbons") 68 | 69 | match = run(session,f"match #{model_pred_name} to #{model_rcsb_name}/{rcsb_chain}") 70 | 71 | ## Color reference structure a diferrent color 72 | run(session,f"color #{model_rcsb_name}/{rcsb_chain} #00FFFF ribbons") 73 | 74 | ## Show only matching chains 75 | run(session,f"show #{model_pred_name} ribbons") 76 | run(session,f"show #{model_rcsb_name}/{rcsb_chain} ribbons") 77 | 78 | ## Orient the chain to view 79 | run(session,"view") 80 | 81 | ## Save match as a new file 82 | run(session,f"save {outdir}/{locus_tag}_{rcsb_match}_{rcsb_chain}.cxs format session") 83 | 84 | quit() -------------------------------------------------------------------------------- /Visualization/Helper_Scripts/color_alphafold.py: -------------------------------------------------------------------------------- 1 | from chimerax.atomic import Structure 2 | from chimerax.core.commands import run 3 | 4 | run(session,"color byattribute bfactor palette orangered:yellow:cyan:blue range 50,100 key true") 5 | run(session,"key pos 0.45,0.1 size 0.5,0.06 justification left labelOffset 5") 6 | run(session,"view") -------------------------------------------------------------------------------- /Visualization/Helper_Scripts/color_rosettafold.py: -------------------------------------------------------------------------------- 1 | from chimerax.atomic import Structure 2 | from chimerax.core.commands import run 3 | 4 | run(session,"color byattribute bfactor palette orangered:yellow:cyan:blue range .5,1 key true") 5 | run(session,"key pos 0.45,0.1 size 0.5,0.06 justification left labelOffset 5") 6 | run(session,"view") -------------------------------------------------------------------------------- /Visualization/Helper_Scripts/restore_chimerax_session.py: -------------------------------------------------------------------------------- 1 | from chimerax.atomic import Structure 2 | from chimerax.core.commands import run 3 | 4 | run(session,"view") 5 | 6 | for m in session.models: 7 | if isinstance(m, Structure): 8 | m._set_chain_descriptions(session) 9 | m._report_chain_descriptions(session) -------------------------------------------------------------------------------- /Visualization/inspect_3D_structures.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ## Pombert Lab, Illinois Tech, 2021 3 | my $name = "inspect_3D_structures.pl"; 4 | my $version = "0.1a"; 5 | my $updated = "2021-07-31"; 6 | 7 | use strict; 8 | use warnings; 9 | use Getopt::Long qw(GetOptions); 10 | use File::Basename; 11 | 12 | my $usage = << "EXIT"; 13 | NAME ${name} 14 | VERSION ${version} 15 | UPDATED ${updated} 16 | 17 | SYNOPSIS The purpose of this script is to visually inspect predicted 3D structures of proteins of interest 18 | 19 | USAGE ${name} \\ 20 | -v 3D_Visualizations 21 | 22 | OPTIONS 23 | -v (--3D_vis) Path to 3D visualizations directory ## created by prepare_visualizations.pl 24 | EXIT 25 | die "\n\n$usage\n\n" unless @ARGV; 26 | 27 | my $indir; 28 | 29 | GetOptions( 30 | "v|3D_vis=s" => \$indir, 31 | ); 32 | 33 | die "\n\n[ERROR]\tPath to 3D visualization directory required\n\n" unless ($indir); 34 | 35 | ## Load all visuals into database for access/reaccess purposes 36 | my %visuals; 37 | opendir (EXT,$indir) or die "\n\n[ERROR]\tCan't open $indir: $!\n\n"; 38 | while (my $locus = readdir(EXT)){ 39 | if (-d "$indir/$locus" && $locus =~ /\w+/){ 40 | opendir (INT,"$indir/$locus") or die "\n\n[ERROR]\tCan't open $indir/$locus: $!\n\n"; 41 | my @files; 42 | while (my $file = readdir(INT)){ 43 | if ($file =~ /\w+/){ 44 | push(@files,"$file"); 45 | } 46 | } 47 | $visuals{$locus} = [@files]; 48 | closedir INT 49 | } 50 | } 51 | 52 | open LOG, ">>", "$indir/visualizations.notes"; 53 | system "clear"; 54 | my ($filename,$dir) = fileparse($0); 55 | my $script = "$dir/Helper_Scripts/restore_chimerax_session.py"; 56 | ## Start visualization 57 | my @loci = sort(keys(%visuals)); 58 | my $pos = 0; 59 | LOOP: while (0==0){ 60 | ## Total amount of options for current locus 61 | my $options = scalar(@{$visuals{$loci[$pos]}}); 62 | ## Infinite loop to allow for typos and unlimited viewing of single locus 63 | ## Escape loop by [a]dvancing, e[x]iting, [r]eviewing previous locus 64 | print "\n\n\tAvailable 3D visualizations for $loci[$pos]:\n\n"; 65 | my $counter = 1; 66 | foreach my $vis (@{$visuals{$loci[$pos]}}){ 67 | print "\t\t$counter. $vis\n"; 68 | $counter++; 69 | } 70 | print "\n\n\tOptions:\n\n"; 71 | if ($options > 1){ 72 | print "\t\t[1-$options] open corresponding file\n"; 73 | } 74 | else { 75 | print "\t\t[1] to open .pdb file\n"; 76 | } 77 | print "\t\t[a] advance to next locus tag\n"; 78 | print "\t\t[p] return to previous locus tag\n"; 79 | print "\t\t[n] to create a note for locus tag\n"; 80 | print "\t\t[x] to exit 3D inspection\n\n"; 81 | print "\t\tSelection: "; 82 | chomp (my $selection = ); 83 | if ($selection eq 'a'){ 84 | system "clear"; 85 | $pos++; 86 | if ($pos > scalar(@loci) - 1){ 87 | $pos = 0; 88 | } 89 | } 90 | elsif ($selection eq 'p'){ 91 | system "clear"; 92 | $pos--; 93 | if ($pos < -1){ 94 | $pos = scalar(@loci) - 2; 95 | } 96 | } 97 | elsif ($selection eq 'x'){ 98 | last LOOP; 99 | } 100 | elsif ($selection eq 'n'){ 101 | print "\n\t\tNotes for $loci[$pos]: "; 102 | chomp(my $notes = ); 103 | if ($notes =~ /\w+/){ 104 | print LOG "$loci[$pos]\t$notes\n"; 105 | } 106 | system "clear"; 107 | } 108 | elsif (($selection =~ /^[0-9]+$/) && (0 < $selection) && ( $selection <= $options)){ 109 | unless ($selection <= $options){ 110 | system "clear"; 111 | print "\n\n\t[ERROR] Invalid Choice: $selection\n"; 112 | } 113 | my $choice = @{$visuals{$loci[$pos]}}[$selection-1]; 114 | ## Adding 2> /dev/null to silence the Release of profile requested but WebEnginePage python warning 115 | system "chimerax 2> /dev/null $indir/$loci[$pos]/$choice $script &"; 116 | system "clear"; 117 | } 118 | else { 119 | system "clear"; 120 | print "\n\n\t[ERROR] Invalid Choice: $selection\n"; 121 | } 122 | } 123 | 124 | print "\n\n\t[EXIT] Terminating 3D Visualization\n\n"; --------------------------------------------------------------------------------