├── INPUT_FORMAT.md ├── LICENSE ├── README.md ├── boltzina ├── __init__.py ├── affinity │ └── predict_affinity.py ├── data │ ├── module │ │ └── inferencev2.py │ ├── parse │ │ └── mmcif.py │ └── write │ │ └── writer.py ├── docking │ ├── calculate_com.py │ └── get_centerofmass.py └── model │ └── models │ └── boltz2.py ├── boltzina_main.py ├── example_usage.py ├── ligand_preparation.py ├── mf-pcba_test.zip ├── preparation_sample ├── config.json └── input_smiles.txt ├── pyproject.toml ├── run.py ├── sample ├── CDK2 │ ├── 1ckp_cdk2.yaml │ ├── boltz_results_base │ │ ├── msa │ │ │ ├── 1ckp_cdk2_0.csv │ │ │ └── 1ckp_cdk2_unpaired_tmp_env │ │ │ │ ├── bfd.mgnify30.metaeuk30.smag30.a3m │ │ │ │ ├── msa.sh │ │ │ │ ├── out.tar.gz │ │ │ │ ├── pdb70.m8 │ │ │ │ └── uniref.a3m │ │ ├── predictions │ │ │ └── 1ckp_cdk2 │ │ │ │ ├── 1ckp_cdk2_model_0.cif │ │ │ │ ├── 1ckp_cdk2_model_0.pdb │ │ │ │ ├── 1ckp_cdk2_model_0_ligand.pdb │ │ │ │ ├── 1ckp_cdk2_model_0_protein.pdb │ │ │ │ ├── affinity_1ckp_cdk2.json │ │ │ │ ├── confidence_1ckp_cdk2_model_0.json │ │ │ │ ├── pae_1ckp_cdk2_model_0.npz │ │ │ │ ├── pde_1ckp_cdk2_model_0.npz │ │ │ │ ├── plddt_1ckp_cdk2_model_0.npz │ │ │ │ └── pre_affinity_1ckp_cdk2.npz │ │ └── processed │ │ │ ├── constraints │ │ │ └── 1ckp_cdk2.npz │ │ │ ├── manifest.json │ │ │ ├── mols │ │ │ └── 1ckp_cdk2.pkl │ │ │ ├── msa │ │ │ └── 1ckp_cdk2_0.npz │ │ │ ├── records │ │ │ └── 1ckp_cdk2.json │ │ │ └── structures │ │ │ └── 1ckp_cdk2.npz │ ├── config.json │ ├── config_scoring.json │ ├── input.txt │ ├── input_pdbs │ │ ├── CDK2_active_0.pdb │ │ ├── CDK2_active_1.pdb │ │ ├── CDK2_active_10.pdb │ │ ├── CDK2_active_11.pdb │ │ ├── CDK2_active_12.pdb │ │ ├── CDK2_active_13.pdb │ │ ├── CDK2_active_14.pdb │ │ ├── CDK2_active_15.pdb │ │ ├── CDK2_active_16.pdb │ │ ├── CDK2_active_17.pdb │ │ ├── CDK2_active_18.pdb │ │ ├── CDK2_active_19.pdb │ │ ├── CDK2_active_2.pdb │ │ ├── CDK2_active_20.pdb │ │ ├── CDK2_active_21.pdb │ │ ├── CDK2_active_22.pdb │ │ ├── CDK2_active_23.pdb │ │ ├── CDK2_active_24.pdb │ │ ├── CDK2_active_25.pdb │ │ ├── CDK2_active_26.pdb │ │ ├── CDK2_active_27.pdb │ │ ├── CDK2_active_28.pdb │ │ ├── CDK2_active_29.pdb │ │ ├── CDK2_active_3.pdb │ │ ├── CDK2_active_30.pdb │ │ ├── CDK2_active_31.pdb │ │ ├── CDK2_active_32.pdb │ │ ├── CDK2_active_33.pdb │ │ ├── CDK2_active_34.pdb │ │ ├── CDK2_active_35.pdb │ │ ├── CDK2_active_36.pdb │ │ ├── CDK2_active_37.pdb │ │ ├── CDK2_active_38.pdb │ │ ├── CDK2_active_39.pdb │ │ ├── CDK2_active_4.pdb │ │ ├── CDK2_active_5.pdb │ │ ├── CDK2_active_6.pdb │ │ ├── CDK2_active_7.pdb │ │ ├── CDK2_active_8.pdb │ │ └── CDK2_active_9.pdb │ ├── input_pdbs_pose │ │ ├── CDK2_active_0_docked.pdb │ │ ├── CDK2_active_1_docked.pdb │ │ ├── CDK2_active_2_docked.pdb │ │ ├── CDK2_active_3_docked.pdb │ │ └── CDK2_active_4_docked.pdb │ └── mols_pose.pkl └── CDK2_ab │ ├── 1ckp_cdk2.yaml │ ├── boltz_results_1ckp_cdk2 │ ├── msa │ │ ├── 1ckp_cdk2_0.csv │ │ ├── 1ckp_cdk2_1.csv │ │ ├── 1ckp_cdk2_paired_tmp_pairgreedy-env │ │ │ ├── out.tar.gz │ │ │ ├── pair.a3m │ │ │ └── pair.sh │ │ └── 1ckp_cdk2_unpaired_tmp_env │ │ │ ├── bfd.mgnify30.metaeuk30.smag30.a3m │ │ │ ├── msa.sh │ │ │ ├── out.tar.gz │ │ │ ├── pdb70.m8 │ │ │ └── uniref.a3m │ ├── predictions │ │ └── 1ckp_cdk2 │ │ │ ├── 1ckp_cdk2_model_0.cif │ │ │ ├── 1ckp_cdk2_model_0.pdb │ │ │ ├── 1ckp_cdk2_model_0_protein.pdb │ │ │ ├── 1ckp_cdk2_model_0_protein_bug.pdb │ │ │ ├── affinity_1ckp_cdk2.json │ │ │ ├── confidence_1ckp_cdk2_model_0.json │ │ │ ├── pae_1ckp_cdk2_model_0.npz │ │ │ ├── pde_1ckp_cdk2_model_0.npz │ │ │ ├── plddt_1ckp_cdk2_model_0.npz │ │ │ └── pre_affinity_1ckp_cdk2.npz │ └── processed │ │ ├── constraints │ │ └── 1ckp_cdk2.npz │ │ ├── manifest.json │ │ ├── mols │ │ └── 1ckp_cdk2.pkl │ │ ├── msa │ │ ├── 1ckp_cdk2_0.npz │ │ └── 1ckp_cdk2_1.npz │ │ ├── records │ │ └── 1ckp_cdk2.json │ │ └── structures │ │ └── 1ckp_cdk2.npz │ └── config.json ├── setup.sh └── setup_boltzina.py /INPUT_FORMAT.md: 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