gdock

Information-driven protein-protein docking using a genetic algorithm

gdock is a fast protein-protein docking tool written in Rust that uses restraints and energy components to guide the docking process. It combines a genetic algorithm with physics-based scoring to find optimal protein-protein complexes.

Note: This project is currently under review for publication in the Journal of Open Source Software (JOSS). A stable v2.0.0 release will follow upon acceptance.

Features

• Fast: Genetic algorithm with early stopping and elitism
• Information-driven: Uses residue restraints to guide docking
• Flexible scoring: Configurable energy weights (VDW, electrostatics, desolvation, restraints)
• Quality metrics: Optional DockQ calculation when reference structure is provided
• Clustering: FCC-based clustering to group similar solutions

Quick Start

# Clone and build
git clone https://github.com/rvhonorato/gdock
cd gdock
cargo build --release

# Run docking with example data
./target/release/gdock run \
  --receptor data/2oob_A.pdb \
  --ligand data/2oob_B.pdb \
  --restraints 933:6,936:8,940:42,941:44,946:45,950:46

Most docking runs complete in ~15 seconds on standard hardware.

Requirements

• Rust (1.70 or later)

Installation

git clone https://github.com/rvhonorato/gdock
cd gdock
cargo build --release

The binary will be available at ./target/release/gdock.

Upon stable release, pre-built binaries and cargo install gdock will also be available.

Usage

gdock has three subcommands: run, score, and restraints.

Docking (run)

Run the full genetic algorithm docking:

gdock run \
  --receptor receptor.pdb \
  --ligand ligand.pdb \
  --restraints 933:6,936:8,940:42

With a reference structure for DockQ calculation:

gdock run \
  --receptor receptor.pdb \
  --ligand ligand.pdb \
  --restraints 933:6,936:8,940:42 \
  --reference native.pdb

Additional options:

• -o, --output-dir <DIR>: Output directory (default: current directory)
• -n, --nproc <NUM>: Number of processors (default: total - 2)
• --no-clust: Disable clustering
• --w_vdw, --w_elec, --w_desolv, --w_air: Custom energy weights

Scoring (score)

Calculate energy components without running the GA:

gdock score \
  --receptor receptor.pdb \
  --ligand ligand.pdb \
  --restraints 933:6,936:8,940:42

Generate restraints (restraints)

Generate restraints from interface contacts in a native structure:

gdock restraints \
  --receptor receptor_ref.pdb \
  --ligand ligand_ref.pdb \
  --cutoff 5.0

Input Format

PDB Files

• Receptor: PDB file containing the receptor protein (single chain)
• Ligand: PDB file containing the ligand protein (single chain)
• Reference (optional): PDB file containing the native complex

Restraints

Comma-separated list of residue pairs in receptor:ligand format:

933:6,936:8,940:42

These indicate which residues should be in contact, based on experimental data or other information sources.

Output

• model_X.pdb: Cluster representatives (unless --no-clust)
• ranked_X.pdb: Top 5 models ranked by score
• metrics.tsv: Tab-separated file with scores and metrics

Output structures can be visualized with molecular viewers such as PyMOL or ChimeraX.

Algorithm

gdock uses:

• Genetic Algorithm: Population of 150, elitism (top 5), tournament selection
• Energy Function: VDW + Electrostatics + Desolvation + AIR restraints
• Restraints: Flat-bottom potential (0-7 Angstrom) for specified residue pairs
• Early Stopping: Converges when no improvement for 10 generations
• Clustering: FCC-based clustering of final population

Testing

Run the test suite:

cargo test

The test suite includes 174 tests covering parsing, energy calculations, and algorithm behavior.

Example

Using the test data included in the repository:

gdock run \
  --receptor data/2oob_A.pdb \
  --ligand data/2oob_B.pdb \
  --restraints 933:6,936:8,940:42,941:44,946:45,950:46 \
  --reference data/2oob.pdb \
  --output-dir results/

This will produce:

• results/model_*.pdb — Cluster representatives ranked by cluster size
• results/ranked_*.pdb — Top 5 models ranked by score
• results/metrics.tsv — Scores and DockQ values for all models

Relevant repositories

• gdock-benchmark: repository containing all scripts and raw data relevant to benchmarking the performance of gdock
• gdock-website: source code for gdock.org

Contributing

Contributions are welcome! Please feel free to submit issues and pull requests on GitHub.

Before submitting a pull request, please ensure:

• All tests pass (cargo test)
• Code is formatted (cargo fmt)
• Linting passes (cargo clippy)

Citation

Coming soon.

License

BSD Zero Clause License. See LICENSE file.