├── .bumpversion.toml ├── .gitignore ├── .readthedocs.yaml ├── CITATION.cff ├── LICENSE ├── Makefile ├── README.md ├── azure-pipelines.yml ├── basic_example_colab.ipynb ├── docs ├── Makefile ├── make.bat ├── paper │ ├── .Rhistory │ ├── Notes.md │ ├── jats │ │ └── paper.jats │ ├── paper.bib │ ├── paper.md │ └── paper.pdf ├── requirements.txt └── source │ ├── _static │ ├── LIS_prot_dna_zn.png │ ├── PAE_amyloid_best.png │ ├── PAE_ligand.png │ ├── PDIA3_clusters_MDS.png │ ├── cluster_PDIA3.png │ ├── dimer.html │ ├── figure_LIS.png │ ├── msa_amyloid.png │ ├── plddt_amyloid.png │ ├── plddt_amyloid_sel.png │ └── show_info.gif │ ├── af_analysis.format.rst │ ├── af_analysis.rst │ ├── af_analysis.test.rst │ ├── analysis.rst │ ├── code_of_conduct.md │ ├── conf.py │ ├── contributing.md │ ├── index.rst │ ├── installation.md │ ├── logo.jpeg │ ├── logo_prompt.txt │ ├── modules.rst │ ├── notebooks │ └── basic_example.ipynb │ └── readme.rst ├── example.ipynb ├── pyproject.toml ├── requirements.txt └── src └── af_analysis ├── __init__.py ├── analysis.py ├── clustering.py ├── data.py ├── docking.py ├── format ├── __init__.py ├── af3_local.py ├── af3_webserver.py ├── afpulldown.py ├── boltz1.py ├── chai1.py ├── colabfold_1_5.py ├── default.py └── massivefold.py ├── plot.py ├── sequence.py └── test ├── __init__.py ├── data_files.py ├── inputs ├── af3_local_prot_pep_complex │ ├── 6zn2_a_b_no_peptide_msa_can │ │ ├── 6zn2_a_b_no_peptide_msa_can_confidences.json │ │ ├── 6zn2_a_b_no_peptide_msa_can_data.json │ │ ├── 6zn2_a_b_no_peptide_msa_can_model.cif │ │ ├── 6zn2_a_b_no_peptide_msa_can_summary_confidences.json │ │ ├── TERMS_OF_USE.md │ │ ├── ranking_scores.csv │ │ ├── seed-1_sample-4 │ │ │ ├── confidences.json │ │ │ ├── model.cif │ │ │ └── summary_confidences.json │ │ ├── seed-2_sample-2 │ │ │ ├── confidences.json │ │ │ ├── model.cif │ │ │ └── summary_confidences.json │ │ └── seed-4_sample-1 │ │ │ ├── confidences.json │ │ │ ├── model.cif │ │ │ └── summary_confidences.json │ └── 7adt_a_u_no_peptide_msa_can │ │ ├── 7adt_a_u_no_peptide_msa_can_confidences.json │ │ ├── 7adt_a_u_no_peptide_msa_can_data.json │ │ ├── 7adt_a_u_no_peptide_msa_can_model.cif │ │ ├── 7adt_a_u_no_peptide_msa_can_summary_confidences.json │ │ ├── TERMS_OF_USE.md │ │ ├── ranking_scores.csv │ │ ├── seed-1_sample-0 │ │ ├── confidences.json │ │ ├── model.cif │ │ └── summary_confidences.json │ │ └── seed-5_sample-4 │ │ ├── confidences.json │ │ ├── model.cif │ │ └── summary_confidences.json ├── beta_amyloid_dimer_cf_1.5.5 │ ├── beta_amyloid_dimer_d2fa3_0.a3m │ ├── beta_amyloid_dimer_d2fa3_0.csv │ ├── beta_amyloid_dimer_d2fa3_0.done.txt │ ├── beta_amyloid_dimer_d2fa3_0_env │ │ ├── bfd.mgnify30.metaeuk30.smag30.a3m │ │ ├── msa.sh │ │ ├── pdb70.m8 │ │ └── uniref.a3m │ ├── beta_amyloid_dimer_d2fa3_0_predicted_aligned_error_v1.json │ ├── beta_amyloid_dimer_d2fa3_0_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_002.pdb │ ├── beta_amyloid_dimer_d2fa3_0_relaxed_rank_002_alphafold2_multimer_v3_model_5_seed_007.pdb │ ├── beta_amyloid_dimer_d2fa3_0_relaxed_rank_003_alphafold2_multimer_v3_model_5_seed_003.pdb │ ├── beta_amyloid_dimer_d2fa3_0_relaxed_rank_004_alphafold2_multimer_v3_model_5_seed_006.pdb │ ├── beta_amyloid_dimer_d2fa3_0_relaxed_rank_005_alphafold2_multimer_v3_model_5_seed_004.pdb │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_001_alphafold2_multimer_v3_model_5_seed_002.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_002_alphafold2_multimer_v3_model_5_seed_007.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_003_alphafold2_multimer_v3_model_5_seed_003.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_004_alphafold2_multimer_v3_model_5_seed_006.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_005_alphafold2_multimer_v3_model_5_seed_004.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_006_alphafold2_multimer_v3_model_5_seed_000.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_007_alphafold2_multimer_v3_model_5_seed_001.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_008_alphafold2_multimer_v3_model_5_seed_005.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_009_alphafold2_multimer_v3_model_4_seed_002.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_010_alphafold2_multimer_v3_model_4_seed_004.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_011_alphafold2_multimer_v3_model_4_seed_006.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_012_alphafold2_multimer_v3_model_3_seed_001.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_013_alphafold2_multimer_v3_model_4_seed_003.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_014_alphafold2_multimer_v3_model_4_seed_007.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_015_alphafold2_multimer_v3_model_3_seed_000.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_016_alphafold2_multimer_v3_model_4_seed_000.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_017_alphafold2_multimer_v3_model_3_seed_006.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_018_alphafold2_multimer_v3_model_3_seed_004.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_019_alphafold2_multimer_v3_model_3_seed_005.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_020_alphafold2_multimer_v3_model_3_seed_002.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_021_alphafold2_multimer_v3_model_3_seed_003.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_022_alphafold2_multimer_v3_model_3_seed_007.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_023_alphafold2_multimer_v3_model_1_seed_001.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_024_alphafold2_multimer_v3_model_1_seed_003.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_025_alphafold2_multimer_v3_model_1_seed_006.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_026_alphafold2_multimer_v3_model_1_seed_000.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_027_alphafold2_multimer_v3_model_1_seed_002.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_028_alphafold2_multimer_v3_model_2_seed_002.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_029_alphafold2_multimer_v3_model_1_seed_004.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_030_alphafold2_multimer_v3_model_1_seed_005.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_031_alphafold2_multimer_v3_model_1_seed_007.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_032_alphafold2_multimer_v3_model_2_seed_001.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_033_alphafold2_multimer_v3_model_2_seed_007.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_034_alphafold2_multimer_v3_model_2_seed_004.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_035_alphafold2_multimer_v3_model_2_seed_006.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_036_alphafold2_multimer_v3_model_2_seed_000.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_037_alphafold2_multimer_v3_model_2_seed_003.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_038_alphafold2_multimer_v3_model_2_seed_005.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_039_alphafold2_multimer_v3_model_4_seed_001.json │ ├── beta_amyloid_dimer_d2fa3_0_scores_rank_040_alphafold2_multimer_v3_model_4_seed_005.json │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_001_alphafold2_multimer_v3_model_5_seed_002.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_002_alphafold2_multimer_v3_model_5_seed_007.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_003.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_006.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_004.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_006_alphafold2_multimer_v3_model_5_seed_000.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_007_alphafold2_multimer_v3_model_5_seed_001.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_008_alphafold2_multimer_v3_model_5_seed_005.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_009_alphafold2_multimer_v3_model_4_seed_002.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_010_alphafold2_multimer_v3_model_4_seed_004.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_011_alphafold2_multimer_v3_model_4_seed_006.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_012_alphafold2_multimer_v3_model_3_seed_001.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_013_alphafold2_multimer_v3_model_4_seed_003.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_014_alphafold2_multimer_v3_model_4_seed_007.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_015_alphafold2_multimer_v3_model_3_seed_000.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_016_alphafold2_multimer_v3_model_4_seed_000.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_017_alphafold2_multimer_v3_model_3_seed_006.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_018_alphafold2_multimer_v3_model_3_seed_004.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_019_alphafold2_multimer_v3_model_3_seed_005.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_020_alphafold2_multimer_v3_model_3_seed_002.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_021_alphafold2_multimer_v3_model_3_seed_003.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_022_alphafold2_multimer_v3_model_3_seed_007.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_023_alphafold2_multimer_v3_model_1_seed_001.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_024_alphafold2_multimer_v3_model_1_seed_003.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_025_alphafold2_multimer_v3_model_1_seed_006.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_026_alphafold2_multimer_v3_model_1_seed_000.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_027_alphafold2_multimer_v3_model_1_seed_002.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_028_alphafold2_multimer_v3_model_2_seed_002.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_029_alphafold2_multimer_v3_model_1_seed_004.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_030_alphafold2_multimer_v3_model_1_seed_005.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_031_alphafold2_multimer_v3_model_1_seed_007.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_032_alphafold2_multimer_v3_model_2_seed_001.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_033_alphafold2_multimer_v3_model_2_seed_007.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_034_alphafold2_multimer_v3_model_2_seed_004.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_035_alphafold2_multimer_v3_model_2_seed_006.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_036_alphafold2_multimer_v3_model_2_seed_000.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_037_alphafold2_multimer_v3_model_2_seed_003.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_038_alphafold2_multimer_v3_model_2_seed_005.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_039_alphafold2_multimer_v3_model_4_seed_001.pdb │ ├── beta_amyloid_dimer_d2fa3_0_unrelaxed_rank_040_alphafold2_multimer_v3_model_4_seed_005.pdb │ ├── cite.bibtex │ ├── config.json │ └── log.txt ├── boltz_results_prot_dna_ligand │ ├── lightning_logs │ │ └── version_0 │ │ │ └── hparams.yaml │ ├── msa │ │ ├── prot_dna_ligand_0.csv │ │ └── prot_dna_ligand_unpaired_tmp_env │ │ │ ├── bfd.mgnify30.metaeuk30.smag30.a3m │ │ │ ├── msa.sh │ │ │ ├── out.tar.gz │ │ │ ├── pdb70.m8 │ │ │ └── uniref.a3m │ ├── predictions │ │ └── prot_dna_ligand │ │ │ ├── confidence_prot_dna_ligand_model_0.json │ │ │ ├── confidence_prot_dna_ligand_model_1.json │ │ │ ├── pae_prot_dna_ligand_model_0.npz │ │ │ ├── pae_prot_dna_ligand_model_1.npz │ │ │ ├── pde_prot_dna_ligand_model_0.npz │ │ │ ├── pde_prot_dna_ligand_model_1.npz │ │ │ ├── plddt_prot_dna_ligand_model_0.npz │ │ │ ├── plddt_prot_dna_ligand_model_1.npz │ │ │ ├── prot_dna_ligand_model_0.cif │ │ │ └── prot_dna_ligand_model_1.cif │ └── processed │ │ ├── manifest.json │ │ ├── msa │ │ └── prot_dna_ligand_0.npz │ │ └── structures │ │ └── prot_dna_ligand.npz ├── chai1_prot_dna_ligand │ ├── msa_depth.pdf │ ├── msas │ │ └── 2977cdfc9dce9bb02f54123934eb59f6669619e8956aebaf7a3690b209afc580.aligned.pqt │ ├── pred.model_idx_0.cif │ ├── pred.model_idx_1.cif │ ├── pred.model_idx_2.cif │ ├── pred.model_idx_3.cif │ ├── pred.model_idx_4.cif │ ├── scores.model_idx_0.npz │ ├── scores.model_idx_1.npz │ ├── scores.model_idx_2.npz │ ├── scores.model_idx_3.npz │ └── scores.model_idx_4.npz ├── chai1_webserver_prot_dna_ligand │ ├── pae.rank_0.npy │ ├── pae.rank_1.npy │ ├── pae.rank_2.npy │ ├── pae.rank_3.npy │ ├── pae.rank_4.npy │ ├── pred.rank_0.cif │ ├── pred.rank_1.cif │ ├── pred.rank_2.cif │ ├── pred.rank_3.cif │ ├── pred.rank_4.cif │ ├── scores.rank_0.json │ ├── scores.rank_1.json │ ├── scores.rank_2.json │ ├── scores.rank_3.json │ └── scores.rank_4.json ├── fold_2024_07_01_12_14_prot_dna_zn │ ├── fold_2024_07_01_12_14_prot_dna_zn.zip │ ├── fold_2024_07_01_12_14_prot_dna_zn_full_data_0.json │ ├── fold_2024_07_01_12_14_prot_dna_zn_full_data_1.json │ ├── fold_2024_07_01_12_14_prot_dna_zn_full_data_2.json │ ├── fold_2024_07_01_12_14_prot_dna_zn_full_data_3.json │ ├── fold_2024_07_01_12_14_prot_dna_zn_full_data_4.json │ ├── fold_2024_07_01_12_14_prot_dna_zn_job_request.json │ ├── fold_2024_07_01_12_14_prot_dna_zn_model_0.cif │ ├── fold_2024_07_01_12_14_prot_dna_zn_model_1.cif │ ├── fold_2024_07_01_12_14_prot_dna_zn_model_2.cif │ ├── fold_2024_07_01_12_14_prot_dna_zn_model_3.cif │ ├── fold_2024_07_01_12_14_prot_dna_zn_model_4.cif │ ├── fold_2024_07_01_12_14_prot_dna_zn_summary_confidences_0.json │ ├── fold_2024_07_01_12_14_prot_dna_zn_summary_confidences_1.json │ ├── fold_2024_07_01_12_14_prot_dna_zn_summary_confidences_2.json │ ├── fold_2024_07_01_12_14_prot_dna_zn_summary_confidences_3.json │ ├── fold_2024_07_01_12_14_prot_dna_zn_summary_confidences_4.json │ └── terms_of_use.md └── ftdmp_beta_amyloid_dimer │ └── jobs │ └── 20f16c00b26b31931c9527ffecbcaea4 │ ├── ids_to_process.txt │ ├── input_hashes │ ├── raw_scoring_results_FGV.txt │ ├── raw_scoring_results_FIGNN.txt │ ├── raw_scoring_results_FIV.txt │ ├── raw_scoring_results_FIVb.txt │ ├── raw_scoring_results_with_ranks.txt │ └── raw_similarity_matrix.txt │ ├── raw_scoring_results_FGV.txt │ ├── raw_scoring_results_FIGNN.txt │ ├── raw_scoring_results_FIV.txt │ ├── raw_scoring_results_FIVb.txt │ ├── raw_scoring_results_with_ranks.txt │ ├── raw_scoring_results_without_ranks.txt │ ├── raw_similarity_matrix.txt │ ├── raw_top_scoring_results_RJS.txt │ ├── raw_top_scoring_results_RJS_diagnostic_cluster_counts_by_threshold.txt │ ├── raw_top_scoring_results_RJS_nonredundant.txt │ ├── 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