├── AlphaFold_multistate.ipynb ├── AlphaFold_multistate_human_kinase_database.ipynb ├── README.md ├── images ├── kinase.confusion_matrix.png └── kinase.confusion_matrix_small.png └── structure_prediction ├── alphafold ├── __init__.py ├── common │ ├── __init__.py │ ├── confidence.py │ ├── protein.py │ ├── protein_test.py │ ├── residue_constants.py │ ├── residue_constants_test.py │ ├── stereo_chemical_props.txt │ └── testdata │ │ └── 2rbg.pdb ├── data │ ├── __init__.py │ ├── feature_processing.py │ ├── mmcif_parsing.py │ ├── msa_identifiers.py │ ├── msa_pairing.py │ ├── parsers.py │ ├── pipeline.py │ ├── pipeline_multimer.py │ ├── templates.py │ └── tools │ │ ├── __init__.py │ │ ├── bio_align.py │ │ ├── hhblits.py │ │ ├── hhsearch.py │ │ ├── hmmbuild.py │ │ ├── hmmsearch.py │ │ ├── jackhmmer.py │ │ ├── kalign.py │ │ └── utils.py ├── model │ ├── __init__.py │ ├── all_atom.py │ ├── all_atom_multimer.py │ ├── all_atom_test.py │ ├── common_modules.py │ ├── config.py │ ├── data.py │ ├── features.py │ ├── folding.py │ ├── folding_multimer.py │ ├── geometry │ │ ├── __init__.py │ │ ├── rigid_matrix_vector.py │ │ ├── rotation_matrix.py │ │ ├── struct_of_array.py │ │ ├── test_utils.py │ │ ├── utils.py │ │ └── vector.py │ ├── layer_stack.py │ ├── layer_stack_test.py │ ├── lddt.py │ ├── lddt_test.py │ ├── mapping.py │ ├── model.py │ ├── modules.py │ ├── modules_multimer.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 ├── notebooks │ ├── __init__.py │ ├── notebook_utils.py │ └── notebook_utils_test.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 ├── colabfold_runner.py ├── conda_create.sh ├── interpolate.py ├── libaf.py ├── libconfig_af.py ├── libmodeller.py ├── openmm.patch ├── requirements.txt ├── run.py ├── run_af.py ├── run_colabfold.py └── run_tbm.py /AlphaFold_multistate.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/AlphaFold_multistate.ipynb -------------------------------------------------------------------------------- /AlphaFold_multistate_human_kinase_database.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/AlphaFold_multistate_human_kinase_database.ipynb -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/README.md -------------------------------------------------------------------------------- /images/kinase.confusion_matrix.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/images/kinase.confusion_matrix.png -------------------------------------------------------------------------------- /images/kinase.confusion_matrix_small.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/images/kinase.confusion_matrix_small.png -------------------------------------------------------------------------------- /structure_prediction/alphafold/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/__init__.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/common/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/common/__init__.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/common/confidence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/common/confidence.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/common/protein.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/common/protein.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/common/protein_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/common/protein_test.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/common/residue_constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/common/residue_constants.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/common/residue_constants_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/common/residue_constants_test.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/common/stereo_chemical_props.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/common/stereo_chemical_props.txt -------------------------------------------------------------------------------- /structure_prediction/alphafold/common/testdata/2rbg.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/common/testdata/2rbg.pdb -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/__init__.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/feature_processing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/feature_processing.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/mmcif_parsing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/mmcif_parsing.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/msa_identifiers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/msa_identifiers.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/msa_pairing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/msa_pairing.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/parsers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/parsers.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/pipeline.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/pipeline_multimer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/pipeline_multimer.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/templates.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/templates.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/tools/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/tools/__init__.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/tools/bio_align.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/tools/bio_align.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/tools/hhblits.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/tools/hhblits.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/tools/hhsearch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/tools/hhsearch.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/tools/hmmbuild.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/tools/hmmbuild.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/tools/hmmsearch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/tools/hmmsearch.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/tools/jackhmmer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/tools/jackhmmer.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/tools/kalign.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/tools/kalign.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/data/tools/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/data/tools/utils.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/__init__.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/all_atom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/all_atom.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/all_atom_multimer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/all_atom_multimer.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/all_atom_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/all_atom_test.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/common_modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/common_modules.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/config.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/data.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/features.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/folding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/folding.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/folding_multimer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/folding_multimer.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/geometry/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/geometry/__init__.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/geometry/rigid_matrix_vector.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/geometry/rigid_matrix_vector.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/geometry/rotation_matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/geometry/rotation_matrix.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/geometry/struct_of_array.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/geometry/struct_of_array.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/geometry/test_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/geometry/test_utils.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/geometry/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/geometry/utils.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/geometry/vector.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/geometry/vector.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/layer_stack.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/layer_stack.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/layer_stack_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/layer_stack_test.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/lddt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/lddt.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/lddt_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/lddt_test.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/mapping.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/mapping.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/model.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/modules.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/modules_multimer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/modules_multimer.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/prng.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/prng.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/prng_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/prng_test.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/quat_affine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/quat_affine.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/quat_affine_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/quat_affine_test.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/r3.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/r3.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/tf/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/tf/__init__.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/tf/data_transforms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/tf/data_transforms.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/tf/input_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/tf/input_pipeline.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/tf/protein_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/tf/protein_features.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/tf/protein_features_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/tf/protein_features_test.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/tf/proteins_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/tf/proteins_dataset.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/tf/shape_helpers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/tf/shape_helpers.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/tf/shape_helpers_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/tf/shape_helpers_test.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/tf/shape_placeholders.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/tf/shape_placeholders.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/tf/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/tf/utils.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/model/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/model/utils.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/notebooks/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/notebooks/__init__.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/notebooks/notebook_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/notebooks/notebook_utils.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/notebooks/notebook_utils_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/notebooks/notebook_utils_test.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/relax/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/relax/__init__.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/relax/amber_minimize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/relax/amber_minimize.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/relax/amber_minimize_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/relax/amber_minimize_test.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/relax/cleanup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/relax/cleanup.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/relax/cleanup_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/relax/cleanup_test.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/relax/relax.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/relax/relax.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/relax/relax_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/relax/relax_test.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/relax/testdata/model_output.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/relax/testdata/model_output.pdb -------------------------------------------------------------------------------- /structure_prediction/alphafold/relax/testdata/multiple_disulfides_target.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/relax/testdata/multiple_disulfides_target.pdb -------------------------------------------------------------------------------- /structure_prediction/alphafold/relax/testdata/with_violations.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/relax/testdata/with_violations.pdb -------------------------------------------------------------------------------- /structure_prediction/alphafold/relax/testdata/with_violations_casp14.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/relax/testdata/with_violations_casp14.pdb -------------------------------------------------------------------------------- /structure_prediction/alphafold/relax/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/relax/utils.py -------------------------------------------------------------------------------- /structure_prediction/alphafold/relax/utils_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/alphafold/relax/utils_test.py -------------------------------------------------------------------------------- /structure_prediction/colabfold_runner.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/colabfold_runner.py -------------------------------------------------------------------------------- /structure_prediction/conda_create.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/conda_create.sh -------------------------------------------------------------------------------- /structure_prediction/interpolate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/interpolate.py -------------------------------------------------------------------------------- /structure_prediction/libaf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/libaf.py -------------------------------------------------------------------------------- /structure_prediction/libconfig_af.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/libconfig_af.py -------------------------------------------------------------------------------- /structure_prediction/libmodeller.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/libmodeller.py -------------------------------------------------------------------------------- /structure_prediction/openmm.patch: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/openmm.patch -------------------------------------------------------------------------------- /structure_prediction/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/requirements.txt -------------------------------------------------------------------------------- /structure_prediction/run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/run.py -------------------------------------------------------------------------------- /structure_prediction/run_af.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/run_af.py -------------------------------------------------------------------------------- /structure_prediction/run_colabfold.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/run_colabfold.py -------------------------------------------------------------------------------- /structure_prediction/run_tbm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huhlim/alphafold-multistate/HEAD/structure_prediction/run_tbm.py --------------------------------------------------------------------------------