# gdock 🦀
**Information-driven protein-protein docking using a genetic algorithm**
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## IMPORTANT
🚧 `gdock` is currently undergoing a full Rust-rewrite 🚧
In its current state it is **not yet production ready**! The code still needs to be reviewed and the protocol needs to be benchmarked.
The older v1.1.0 python version is still available in the releases.
---
<img src="imgs/gdock_logo.png" width="350">
gdock is a fast, efficient 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.
## 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
- 🦀 **Rust-powered**: Memory-safe and high-performance
## Installation
```bash
git clone https://github.com/gdocking/gdock
cd gdock
cargo build --release
```
The binary will be available at `./target/release/gdock`.
## Usage
### Basic Usage (Docking Mode)
Run the full genetic algorithm docking:
```bash
gdock \
--receptor data/A.pdb \
--ligand data/B.pdb \
--restraints 933:6,936:8,940:42,941:44,946:45,950:46
```
This will:
- Dock the ligand onto the receptor using the genetic algorithm
- Use the specified residues to create restraints
- Optimize based on energy scoring
- Output `best_by_score.pdb`
### With Reference Structure (DockQ Mode)
When you have a reference/native structure for validation:
> This is only useful in parametrization scenarios or when you are comparing `gdock`.
> Since in a real scenario you will not have the actual reference.
```bash
gdock \
--receptor data/A.pdb \
--ligand data/B.pdb \
--restraints 933:6,936:8,940:42,941:44,946:45,950:46 \
--reference data/2oob.pdb
```
This will:
- Calculate DockQ, RMSD, iRMSD, and FNAT during optimization
- Output both `best_by_score.pdb` and `best_by_dockq.pdb`
### Score-Only Mode
Calculate energy components without running the GA:
```bash
gdock \
--receptor data/A.pdb \
--ligand data/B.pdb \
--restraints 933:6,936:8,940:42,941:44,946:45,950:46 \
--score
```
This will quickly compute VDW, electrostatic, desolvation, and AIR energies for the given complex.
### Custom Energy Weights
```bash
gdock \
--receptor data/A.pdb \
--ligand data/B.pdb \
--restraints 933:6,936:8,940:42,941:44,946:45,950:46 \
--w_vdw 1.0 \
--w_elec 0.5 \
--w_desolv 0.1 \
--w_air 100.0
```
## 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 (both chains)
### Restraints
- Colon-separated list of pairs of residue numbers in `receptor:ligand` format: `933:6,936:8`, etc
- Indicates which residues should be part of the interaction, based on experimental data or other information source
- Creates all pairwise restraints between receptor and ligand residues
- More restraints = stronger guidance but may be restrictive!
## Output
- `best_by_score.pdb`: Complex with the best energy score
- `best_by_dockq.pdb`: Complex with the best DockQ (only with `--reference`)
## Algorithm
gdock uses:
- **Genetic Algorithm**: Population of 150, elitism (top 5), tournament selection
- **Energy Function**: VDW + Electrostatics + Desolvation + AIR restraints
- **Restraints**: Flat-bottom potential (0-7Ã…) for specified residue pairs
- **Early Stopping**: Converges when no improvement for 10 generations
## Citation
Coming soon.
## License
See LICENSE file.