| { |
| "confidence": { |
| "boltz2": "pair_chains_iptm[0][1]; native ligand_iptm retained separately because heme is also a ligand entity", |
| "chai1": "per_chain_pair_iptm[0,0,1]", |
| "esmfold2": "pair_chains_iptm[0,1]", |
| "openfold3": "chain_pair_iptm[(A, L)]", |
| "primary_field": "directed protein-to-intended-ligand chain-pair iPTM", |
| "protenix_v1": "chain_pair_iptm[0][1]" |
| }, |
| "coordinate_alignment": { |
| "aligned_coordinate_root": "structures/predicted", |
| "anchor_count": 187, |
| "anchor_map": "anchor_map.csv", |
| "coordinate_action": "One rigid transform applied to every atom; ligand, heme, pocket fitting, trimming and remapping are excluded.", |
| "fit": "proper-rotation Kabsch over frozen C-alpha correspondences", |
| "invariant": "cyp3a4_1tqn_conserved_scaffold_ca_v1", |
| "numbering": { |
| "CYP1A2": "generated index 1 maps to UniProt 27", |
| "CYP2C9": "generated index 1 maps to UniProt 30", |
| "CYP2D6": "generated index 1 maps to UniProt 34", |
| "CYP3A4": "generated index 1 maps to UniProt 30" |
| }, |
| "reference": "1TQN chain A" |
| }, |
| "name": "cyp_cofold_postprocess_20260804", |
| "scoring": { |
| "add_mdl_contacts": false, |
| "class": "ost.mol.alg.ligand_scoring_lddtpli.LDDTPLIScorer", |
| "metric": "ost_lddt_pli", |
| "model_ligand": "intended crystal-ligand chain only; heme excluded", |
| "model_receptor": "generated chain A peptide", |
| "no_score_policy": "Retain NO_ASSIGNMENT; no proxy or imputation.", |
| "radius_A": 6.0, |
| "software": "OpenStructure 2.11.1", |
| "substructure_match": false, |
| "target_ligand": "manifest-selected CCD copy in author chain A, or the exact governed residue for the 10-system pilot", |
| "target_receptor": "truth crystal author chain A peptide", |
| "thresholds_A": [ |
| 0.5, |
| 1.0, |
| 2.0, |
| 4.0 |
| ] |
| }, |
| "selector_analysis": { |
| "candidate_counts": { |
| "boltz2": 20, |
| "chai1": 20, |
| "esmfold2": 50, |
| "openfold3": 20, |
| "protenix_v1": 20 |
| }, |
| "metrics": [ |
| "within-system Spearman rho", |
| "top-iPTM uplift over ensemble-mean LDDT-PLI", |
| "top-iPTM truth percentile", |
| "oracle-minus-selected regret" |
| ], |
| "passed_only_sensitivity": "method_selector_summary_passed_cells.csv", |
| "primary_scope": "complete method-system cells only", |
| "uncertainty": "5000 system-level bootstrap replicates; seed 20260804" |
| } |
| } |
|
|
