├── .gitignore ├── DeepUrfold-updated_results ├── README.txt ├── embedding_vs_tm │ ├── concatenated_model │ │ └── EMbedding dist vs TM.ipynb │ ├── global_model │ │ ├── .ipynb_checkpoints │ │ │ ├── Embedding vs tm-Copy1-checkpoint.ipynb │ │ │ └── Embedding vs tm-checkpoint.ipynb │ │ └── Embedding vs tm.ipynb │ └── sh3_only │ │ └── Embedding vs tm.ipynb ├── permutations_and_fragments │ ├── Make Figure 2-newperm.ipynb │ └── Make Figure 2.ipynb └── test_rotations │ ├── concatenated model │ └── concated_model_distances.ipynb │ ├── global_model │ └── Distance_cosine.ipynb │ └── sh3_only │ ├── Random_rots_vs_sh3_model.ipynb │ ├── run_elbo_cmd.sh │ ├── run_latent_cmd.sh │ └── single sh3 umap distance.ipynb ├── DeepUrfold ├── Analysis │ ├── AllVsAll │ │ ├── Random.py │ │ ├── SequenceBased │ │ │ ├── EVcouplings.py │ │ │ ├── __init__.py │ │ │ ├── deepsequence.py │ │ │ ├── deepsequence_config.txt │ │ │ ├── esm_ava.py │ │ │ ├── hmmer.py │ │ │ ├── mmseqs.py │ │ │ ├── run_deepsequence.py │ │ │ ├── seqdesign.py │ │ │ └── uclust.py │ │ ├── StructureBased │ │ │ ├── __init__.py │ │ │ ├── biozernike.py │ │ │ ├── deepurfold_ava.py │ │ │ ├── deepurfold_ava_onemodel.py │ │ │ ├── maxcluster.py │ │ │ ├── struct2seq.py │ │ │ └── tmalign.py │ │ └── __init__.py │ ├── Clustering.py │ ├── CosineSimilarity.py │ ├── ExploreLatenLocal.py │ ├── ExploreLatent.py │ ├── ExploreLatentGW.py │ ├── KernelDensityEstimate.py │ ├── KernelDesnityEstimate_rebuttal2.py │ ├── LRP.py │ ├── SBMDrawer.py │ ├── StochasticBlockModel.py │ ├── Webapp │ │ ├── .Rhistory │ │ ├── README.md │ │ ├── __init__.py │ │ ├── data │ │ │ ├── bp.csv │ │ │ ├── cc.csv │ │ │ ├── flare-cath.csv │ │ │ ├── flare-cath.csv2 │ │ │ ├── flare.csv │ │ │ ├── flare2.csv │ │ │ ├── flare_links.csv │ │ │ ├── flare_links.csv.old │ │ │ ├── go-basic.obo │ │ │ └── mf.csv │ │ ├── freeze.py │ │ ├── old │ │ │ ├── flare.csv │ │ │ └── flare_links.csv │ │ ├── old2 │ │ │ ├── 1a04A02.json │ │ │ ├── 1jpy.cif │ │ │ ├── 2domain_communities.json │ │ │ ├── 3domain_communities.json │ │ │ ├── d3Chart.js │ │ │ ├── domain_communities.json │ │ │ ├── grid.html │ │ │ ├── heatmap.js │ │ │ └── index.html │ │ ├── static │ │ │ ├── css │ │ │ │ ├── bootstrap-table.min.css │ │ │ │ └── index.css │ │ │ └── js │ │ │ │ ├── bootstrap-table.min.js │ │ │ │ ├── d3.v5.min.js │ │ │ │ ├── index.js │ │ │ │ └── radial_tree.js │ │ ├── templates │ │ │ └── index.html │ │ └── zoomable-circle-packing │ │ │ ├── 5831f55fccfa1c41@165.js │ │ │ ├── LICENSE.txt │ │ │ ├── README.md │ │ │ ├── index.html │ │ │ ├── index.js │ │ │ ├── inspector.css │ │ │ ├── package.json │ │ │ └── runtime.js │ ├── __init__.py │ ├── fuzzle.py │ ├── loss.py │ └── sbm.py ├── DataModules │ ├── DDIBindingSiteDataModule.py │ ├── DistributedDomainStructureDataModule.py │ ├── DomainStructureDataModule.py │ ├── ProteinMPNNDataModule.py │ └── __init__.py ├── Evaluators │ ├── EvaluateDistrubutedDomainStructureVAE.py │ ├── EvaluateDomainStructureVAE.py │ ├── Evaluator.py │ └── __init__.py ├── FeatureSelection │ ├── config.yaml │ ├── feature_selection_all.yaml │ ├── feature_selection_groups.yaml │ ├── ig_vaew_sweep.yaml │ ├── sweep.yaml │ └── wandb_sweep.sh ├── Metrics │ ├── AUCPRC.py │ ├── AUROC.py │ ├── ClassifactionMetricSaver.py │ ├── LRPSaver.py │ ├── MetricSaver.py │ ├── RawMetricSaver.py │ ├── __init__.py │ ├── functional.py │ ├── raw_metric.py │ └── relevance.py ├── Models │ ├── BindingSitePredictor.py │ ├── DataParallel.py │ ├── DomainStructureAEKL.py │ ├── DomainStructureSegmentationModel.py │ ├── DomainStructureVAE.py │ ├── MinkowskiConvolution.py │ ├── MinkowskiLeakyReLU.py │ ├── Models.py │ ├── Models2.py │ ├── SuperfamilyAE.py │ ├── UNetDropout.py │ ├── __init__.py │ ├── classification.py │ ├── metric.py │ ├── minkae.py │ ├── minkresnet.py │ ├── minkresnet_block.py │ ├── minkunet.py │ ├── minkunet_do_relu.py │ ├── minkvae.py │ └── van_der_waals_surface.py ├── Trainers │ ├── DistributedTrainSuperfamilyVAE.py │ ├── Train.py │ ├── TrainBindingSitePredictor.py │ ├── TrainSuperfamilyAE.py │ ├── TrainSuperfamilyVAE.py │ └── __init__.py ├── __init__.py ├── figures │ ├── 1bkbA02_segments.txt │ ├── 1bkbA02_vs_MLP.png │ ├── 1bkbA02_vs_MLP.pse │ ├── 1bkbA02_vs_TERMA116.png │ ├── 1bkbA02_vs_TERMA116.pse │ ├── 1kq2A00_vs_MLP.png │ ├── 1kq2A00_vs_MLP.pse │ ├── 1u1sA00_segments.txt │ ├── 1uebA03_vs_MLP.png │ └── 1uebA03_vs_MLP.pse ├── scripts │ ├── __init__.py │ ├── alter_ss.py │ ├── cluster.py │ ├── create_datasets.py │ ├── create_datasets.sh │ ├── deloop_dataset.py │ ├── ex_feature_selection_runs.txt │ ├── features.txt │ ├── filter_h5.py │ ├── kolodnt_themes.csv │ ├── parse_kolodny_themes.py │ ├── rearrange_ss.py │ ├── rearrange_ss_strand_reversal.py │ ├── run_one_feature.sh │ ├── run_umap.py │ ├── setup_lambdalabs.sh │ └── train_sfams_loop.sh └── util │ ├── __init__.py │ ├── distrib_data_parallel.py │ └── wandb.py ├── Docker ├── Dockerfile └── Makefile ├── Kubeflow ├── config.yml ├── hsds_deployment.yml ├── hsds_pvc.yml ├── hsds_service.yml ├── 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