| run: | |
| name: experimental_validation | |
| output_dir: results/experimental_validation_strict | |
| max_batches: 2 | |
| random_seed: 42 | |
| data: | |
| target_id: mdm2_pocket_excerpt | |
| target_path: data/targets/mdm2_1ycr_pocket_excerpt.pdb | |
| ligand_table: data/ligands/mdm2_ligands_validation_strict.csv | |
| benchmark_metadata: data/benchmarks/mdm2_validation_metadata.json | |
| backend: | |
| type: rdock | |
| allow_mock_if_missing: false | |
| require_real_backend: true | |
| n_runs: 1 | |
| mapper_radius: 6.0 | |
| command_timeout_seconds: 60 | |
| encoding: | |
| fingerprint_radius: 2 | |
| fingerprint_bits: 1024 | |
| generate_3d: true | |
| clustering: | |
| butina_cutoff: 0.35 | |
| n_hyperclusters: 4 | |
| scheduler: | |
| batch_size: 6 | |
| init_coverage_fraction: 0.34 | |
| conservative_deprioritize: true | |
| scoring: | |
| interface_weight: 1.0 | |