File size: 1,718 Bytes
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name: experimental_benchmark_single_library
output_dir: results/experimental_benchmark_single_library
random_seed: 42
adaptive_budget: 1500
baseline_budget: 1500
batch_size: 10
max_batches: 200
target:
protein_name: MDM2
target_id: mdm2_experimental_single_library
docking_reference_pdb: 4HG7
docking_target_path: data/targets/experimental_benchmark_single_library/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_single_library
reuse_existing: true
per_reference_target: 1300
pubchem_similarity_threshold: 80
pubchem_max_records: 2500
min_similarity_keep: 0.2
shared_library_target_size: 1500
analog_similarity_threshold: 0.65
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:
rolling_window: 100
analog_similarity_threshold: 0.65
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