pandadock - Main Docking Command

The pandadock command is the primary interface for molecular docking in PandaDock.

Synopsis

pandadock COMMAND [OPTIONS]

Commands

dock - Traditional molecular docking with Vina-style scoring
hybrid - Hybrid docking: pose generation + GNN rescoring (recommended)
list-algorithms - Show available algorithms and scoring functions
gnn - GNN subcommands (train, predict, benchmark, compare)

pandadock dock

Performs molecular docking using hierarchical search with Vina-style scoring.

Required Options:

-r, --receptor PATH: Receptor PDB file (protein structure)
-l, --ligand PATH: Ligand file (SDF, MOL2, or PDB format)
--center X Y Z or --grid-config PATH: Grid box specification. Either provide center coordinates (in Angstroms) or a JSON configuration file.
--box X Y Z: Grid box dimensions (in Angstroms). Required if --center is used.

Scoring Options:

-s, --scoring FUNCTION

Scoring function to use. Default: vina

Available:

vina - Vina-style empirical scoring (recommended)
physics_based - Physics-based Lennard-Jones + electrostatics

--rescoring METHOD

Rescoring method for top poses. Default: none

Options: none, mmgbsa

Output Options:

-o, --output-dir PATH: Output directory for results. Default: docking_output
-n, --num-poses N: Number of poses to generate. Default: 20
--visualize / --no-visualize: Generate visualization plots. Default: enabled

Performance Options:

--fast: Enable fast mode with reduced sampling for quick testing
--ensemble / --no-ensemble: Use Boltzmann ensemble averaging. Default: enabled

Example:

pandadock dock -r protein.pdb -l ligand.sdf \
               --center 10 20 30 --box 20 20 20 \
               -o results/

pandadock hybrid

Recommended workflow for best accuracy. Combines traditional pose generation with SE(3)-equivariant GNN rescoring.

Required Options:

-r, --receptor PATH: Receptor PDB file
-l, --ligand PATH: Ligand file (SDF, MOL2, or PDB format)
--center X Y Z or --grid-config PATH: Grid box specification
--box X Y Z: Grid box dimensions
-m, --model PATH: Path to trained GNN model checkpoint

Optional Options:

-o, --output-dir PATH: Output directory. Default: hybrid_output
-n, --num-poses N: Number of poses to generate for rescoring. Default: 50
--top-k N: Number of top poses to keep after rescoring. Default: 10
--fast: Use fast mode with reduced sampling

Example:

pandadock hybrid -r protein.pdb -l ligand.sdf \
                 --center 10 20 30 --box 20 20 20 \
                 -m models/best_model.pt \
                 -o hybrid_results/

Output:

The hybrid command generates:

hybrid_results.csv - Rankings with GNN and Vina scores
pose_1_pec50_X.XX.pdb - Top poses with pEC50 in filename
complex_1.pdb, etc. - Protein-ligand complexes

pandadock gnn

GNN subcommands for training and prediction. See pandadock gnn - GNN Commands Reference for details.

pandadock gnn train - Train GNN model
pandadock gnn predict - Predict binding affinity
pandadock gnn benchmark - Benchmark model performance
pandadock gnn compare - Compare against baselines

pandadock list-algorithms

Show available docking algorithms and scoring functions.

pandadock list-algorithms

Output Files

dock command:

complex1.pdb, complex2.pdb, ... - Protein-ligand complexes (top 10)
pose1.pdb, pose2.pdb, ... - Ligand poses only (top 10)
docking_results.json - Complete results with energies
interaction_analysis.json - Detailed interaction analysis
binding_affinities.png - Affinity distribution plot

hybrid command:

hybrid_results.csv - Rankings with GNN and Vina scores
pose_N_pec50_X.XX.pdb - Top pose structures
complex_N.pdb - Protein-ligand complexes

Global Options

-v, --verbose: Enable verbose logging
--version: Show version information
-h, --help: Show help message

Examples

Basic Docking:

pandadock dock -r protein.pdb -l ligand.sdf \
               --center 10 20 30 --box 20 20 20

Hybrid Docking (Recommended):

pandadock hybrid -r protein.pdb -l ligand.sdf \
                 --center 10 20 30 --box 20 20 20 \
                 -m models/best_model.pt

Fast Screening:

pandadock dock -r protein.pdb -l ligand.sdf \
               --center 10 20 30 --box 20 20 20 \
               --fast --num-poses 10

With MM-GBSA Rescoring:

pandadock dock -r protein.pdb -l ligand.sdf \
               --center 10 20 30 --box 20 20 20 \
               --rescoring mmgbsa