| { |
| "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/" |
| } |
|
|
