├── LICENSE ├── README.md ├── enzdes_utils └── fast_design.py ├── hemoprotein_biocatalysts_design ├── scripts_fast_design │ ├── fast_design_to_relax.py │ ├── generate_design_scores_table.py │ ├── generate_design_slurm_scripts.py │ ├── plot_score_distribution.py │ ├── remove_empty_design_folders.py │ └── run_design.sh ├── scripts_fast_relax │ ├── fast_design_relax.pbs │ ├── fast_relax.pbs │ ├── generate_relax_scores_table.py │ ├── generate_relax_scores_table_multi_scaf.py │ ├── generate_relax_slurm_scripts.py │ └── get_best_relaxed_decoys.py ├── scripts_multi-state_design │ ├── heat_map.py │ ├── logo_plot.py │ ├── multistate_design_fitness.argmin.py │ ├── multistate_design_fitness.softmin.py │ ├── site-saturation_mutagenesis.benzofuran.pbs │ ├── site-saturation_mutagenesis.pCF3.pbs │ └── site-saturation_mutagenesis.pbs ├── scripts_preprocess_pdb │ ├── check_relax_jobs.py │ ├── classify_hemoprotein_folds.py │ ├── clean_hemoprotein_pdb.py │ ├── generate_hemoprotein_substrate_complexes.py │ ├── get_the_best_decoy.py │ ├── grab_pdb_info.py │ ├── redundancy_check.py │ └── relax_new_pdb.sh └── substrates │ ├── cyclopropanation_benzofuran_EDA │ ├── HEM-TS-1R2R.cst │ ├── HEM-TS-1R2S.cst │ ├── HEM-TS-1S2R.cst │ ├── HEM-TS-1S2S.cst │ ├── RRT.params │ ├── RRT.pdb │ ├── RST.params │ ├── RST.pdb │ ├── SRT.params │ ├── SRT.pdb │ ├── SST.params │ └── SST.pdb │ ├── cyclopropanation_p-CF3-styrene_EDA │ ├── HEM-TS-1R2R.cst │ ├── HEM-TS-1R2S.cst │ ├── HEM-TS-1S2R.cst │ ├── HEM-TS-1S2S.cst │ ├── RRT.params │ ├── RRT.pdb │ ├── RST.params │ ├── RST.pdb │ ├── SRT.params │ ├── SRT.pdb │ ├── SST.params │ └── SST.pdb │ └── cyclopropanation_styrene_EDA │ ├── HEM-TS-1R2R.cst │ ├── HEM-TS-1R2S.cst │ ├── HEM-TS-1S2R.cst │ ├── HEM-TS-1S2S.cst │ ├── RRT.params │ ├── RRT.pdb │ ├── RST.params │ ├── RST.pdb │ ├── SRT.params │ ├── SRT.pdb │ ├── SST.params │ └── SST.pdb └── protein_stapling ├── README.md ├── ligands ├── O2beY-ASP │ ├── ASX.params │ ├── O2beY-ASP.cst │ ├── O2beY-ASP_Relax.cst │ └── subs.flags ├── O2beY-CYS │ ├── CYX.params │ ├── O2beY-CYS.cst │ ├── O2beY-CYS_Relax.cst │ ├── OBY.params │ ├── OBY.rotlib.pdb │ ├── TYZ.params │ └── subs.flags ├── O2beY-GLU │ ├── GLX.params │ ├── O2beY-GLU.cst │ ├── O2beY-GLU_Relax.cst │ └── subs.flags ├── O2beY-HIS │ ├── HIX.params │ ├── O2beY-HIS.cst │ ├── O2beY-HIS_Relax.cst │ └── subs.flags └── O2beY-LYS │ ├── LYX.params │ ├── O2beY-LYS.cst │ ├── O2beY-LYS_Relax.cst │ └── subs.flags ├── pdbantibody └── 7l6v │ ├── 7l6v-A-B-unbound.pdb │ ├── 7l6v-A-B-unbound_relaxed.pdb │ ├── 7l6v-A-B.npz │ ├── 7l6v-A-B.pdb │ └── 7l6v-A-B_relaxed.pdb ├── pdbyCD └── 1ysb │ ├── 1ysb-A-B.pdb │ ├── 1ysb-A-B_relaxed.pdb │ ├── 1ysb-A.pdb │ ├── 1ysb-A_relaxed.pdb │ ├── 1ysb-B.pdb │ └── 1ysb-B_relaxed.pdb ├── scripts-design ├── esm_scoring_staple.py ├── fast_design.pbs ├── fast_design_2_mpnn.py ├── fast_relax.pbs ├── fast_relax_unbound.pbs ├── generate_unbound_pdb.py ├── generate_unbound_wt_pdb.py ├── mpnn.pbs ├── mpnn_2_fast_relax.py └── relax.pbs ├── 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