├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── Representations_AlphaFold2PredictStructure.ipynb ├── Representations_AlphaFold2_v3.ipynb ├── alphafold ├── __init__.py ├── common │ ├── __init__.py │ ├── confidence.py │ ├── protein.py │ ├── protein_test.py │ ├── residue_constants.py │ ├── residue_constants_test.py │ └── testdata │ │ └── 2rbg.pdb ├── data │ ├── __init__.py │ ├── mmcif_parsing.py │ ├── parsers.py │ ├── pipeline.py │ ├── templates.py │ └── tools │ │ ├── __init__.py │ │ ├── hhblits.py │ │ ├── hhsearch.py │ │ ├── hmmbuild.py │ │ ├── hmmsearch.py │ │ ├── jackhmmer.py │ │ ├── kalign.py │ │ └── utils.py ├── model │ ├── __init__.py │ ├── all_atom.py │ ├── all_atom_test.py │ ├── common_modules.py │ ├── config.py │ ├── data.py │ ├── features.py │ ├── folding.py │ ├── layer_stack.py │ ├── layer_stack_test.py │ ├── lddt.py │ ├── lddt_test.py │ ├── mapping.py │ ├── model.py │ ├── modules.py │ ├── prng.py │ ├── prng_test.py │ ├── quat_affine.py │ ├── quat_affine_test.py │ ├── r3.py │ ├── tf │ │ ├── __init__.py │ │ ├── data_transforms.py │ │ ├── input_pipeline.py │ │ ├── protein_features.py │ │ ├── protein_features_test.py │ │ ├── proteins_dataset.py │ │ ├── shape_helpers.py │ │ ├── shape_helpers_test.py │ │ ├── shape_placeholders.py │ │ └── utils.py │ └── utils.py └── relax │ ├── __init__.py │ ├── amber_minimize.py │ ├── amber_minimize_test.py │ ├── cleanup.py │ ├── cleanup_test.py │ ├── relax.py │ ├── relax_test.py │ ├── testdata │ ├── model_output.pdb │ ├── multiple_disulfides_target.pdb │ ├── with_violations.pdb │ └── with_violations_casp14.pdb │ ├── utils.py │ └── utils_test.py ├── docker ├── Dockerfile ├── openmm.patch ├── requirements.txt └── run_docker.py ├── header.jpg ├── imgs ├── casp14_predictions.gif └── header.jpg ├── notebooks └── AlphaFold.ipynb ├── requirements.txt ├── run_alphafold.py ├── run_alphafold_test.py ├── scripts ├── download_all_data.sh ├── download_alphafold_params.sh ├── download_bfd.sh ├── download_mgnify.sh ├── download_pdb70.sh ├── 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