Datasets:
File size: 2,391 Bytes
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"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"
}
}
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