| run: | |
| name: experimental_benchmark | |
| output_dir: results/experimental_benchmark | |
| random_seed: 42 | |
| max_batches: 15 | |
| batch_size: 10 | |
| adaptive_budget: 150 | |
| baseline_budget: 150 | |
| resume: true | |
| target: | |
| protein_name: MDM2 | |
| target_id: mdm2_experimental | |
| docking_reference_pdb: 4HG7 | |
| docking_target_path: data/targets/experimental_benchmark/mdm2_4hg7.pdb | |
| references: | |
| complexes: | |
| - pdb_id: 4HG7 | |
| ligand_comp_id: NUT | |
| reference_id: ref_nutlin3a | |
| - pdb_id: 4J7D | |
| ligand_comp_id: I31 | |
| reference_id: ref_ro5045331 | |
| - pdb_id: 4LWU | |
| ligand_comp_id: 20U | |
| reference_id: ref_ro5499252 | |
| benchmark_dataset: | |
| output_dir: data/ligands/experimental_benchmark | |
| reuse_existing: true | |
| per_reference_target: 1500 | |
| pubchem_similarity_threshold: 80 | |
| pubchem_max_records: 2200 | |
| min_similarity_keep: 0.2 | |
| backend: | |
| require_real_backend: true | |
| allow_mock_if_missing: false | |
| n_runs: 1 | |
| mapper_radius: 6.0 | |
| command_timeout_seconds: 180 | |
| encoding: | |
| fingerprint_radius: 2 | |
| fingerprint_bits: 1024 | |
| generate_3d: false | |
| clustering: | |
| butina_cutoff: 0.35 | |
| n_hyperclusters: 20 | |
| scheduler: | |
| init_coverage_fraction: 0.35 | |
| conservative_deprioritize: true | |
| model_weight_schedule: | |
| sample_knots: [20, 50, 100, 200] | |
| weight_knots: [0.1, 0.3, 0.5, 0.8] | |
| max_weight: 0.9 | |
| min_weight: 0.05 | |
| instability_threshold: 2.0 | |
| instability_decay: 0.25 | |
| surrogate: | |
| prefer_xgboost: true | |
| n_estimators: 200 | |
| min_train_samples: 12 | |
| max_depth_small: 3 | |
| max_depth_large: 6 | |
| analysis: | |
| analog_similarity_threshold: 0.65 | |
| topk_values: [10, 25, 50, 100] | |