{
  "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/"
}