Datasets:
File size: 2,098 Bytes
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"release": "AlphaEnzyme",
"tasks": {
"specificity": {
"tables": [
"inputs/specificity/tables/train.csv",
"inputs/specificity/tables/valid.csv",
"inputs/specificity/eval/eval.csv"
],
"reference_banks": [
"inputs/specificity/features/reference/positive_context.npz",
"inputs/specificity/features/reference/positive_protein_pocket.npz"
],
"reaction_fingerprints": "inputs/specificity/features/drfp/reaction_fingerprints.pkl"
},
"kinetics": {
"tables": [
"inputs/kinetics/train.csv",
"inputs/kinetics/valid.csv",
"inputs/kinetics/test.csv"
],
"sources": "inputs/kinetics/alpha_sources.json",
"row_extra": [
"inputs/kinetics/alpha_train_row_extra.npz",
"inputs/kinetics/alpha_valid_row_extra.npz",
"inputs/kinetics/alpha_test_row_extra.npz"
],
"training_stats": "inputs/kinetics/alpha_training_zscore_stats.npz",
"substrate_fingerprints": "inputs/kinetics/features/substrate/substrate_fp_ecfp4_2048.pkl",
"reaction_fingerprints": "inputs/kinetics/features/drfp/rxn2fp_public_kinetics.pkl",
"protein_pocket_bank": "inputs/kinetics/features/protein_pocket/all_protein_pocket.npz"
},
"mutation": {
"labels": "inputs/mutation/inputs/rows.csv",
"variants": "inputs/mutation/variants.csv",
"references": "inputs/mutation/references.csv",
"full_raw_table": "inputs/mutation/proteingym_rows.csv",
"folds": "inputs/mutation/folds.json",
"protocol": "inputs/mutation/protocol.json",
"component_scores": "inputs/mutation/component_inputs_unlabelled.csv",
"fold_normalization": "inputs/mutation/features/fold_*_normalization.npz"
}
},
"precomputed_features": "Not included. Generate Pairformer/ESMC features from the raw tables with code/scripts/data_preprocessing/prepare_pairs.py; see docs/NEW_DATA.md.",
"checkpoints": "Distributed separately in AlphaEnzyme_checkpoints.zip.",
"path_base": "Repository root after unzipping the data archive into data/"
}
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