Software Tools
Our group develops open-source software tools for computational structural biology research. All tools are freely available on GitHub.
gRINN
A tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations. gRINN calculates pairwise residue interaction energies from GROMACS MD trajectories and builds energy-based protein networks.
- Trajectory and ensemble analysis modes
- Electrostatic and van der Waals energy calculations
- Protein Energy Network (PEN) construction
- Interactive web dashboard for 3D visualization
PocketHunter
A command-line tool for detecting and analyzing potential small molecule binding sites in protein molecular simulation trajectories. PocketHunter identifies druggable pockets including cryptic binding sites that appear during protein dynamics.
- Binding site detection from MD trajectories
- Cryptic pocket identification
- Pocket clustering across frames
- Interactive residue composition heatmaps
consensus_docking
A molecular docking pipeline that runs multiple docking tools simultaneously and compares their results. Automates protein-ligand docking by orchestrating several docking engines with consensus analysis.
- Multi-tool docking (Smina, Gnina, LeDock, GOLD)
- Adaptive exhaustiveness optimization
- RMSD analysis across docking tools
- Automated file conversions and pose extraction