VDock software package
- Intuitive graphical user interface (GUI) to protein-ligand docking calculation engine
- Guided workflow: system setup, run docking calculations, results analysis
- Seamless setup and docking direct from import of raw protein PDB file and ligand series SD file
- All atom forcefield available as well as united atom
- Flexible ligand and optionally flexible protein side chains
- Run docking calculations directly on desktop or export calculations to HPC
- Optionally, a ligand template/ligand co-crystal can define search box placement
- Multiple search techniques: Global Underestimator Methods, Genetic Algorithms, Poling, and Tabu Search
- Post-docking calculation analysis, including visualization of multiple docked conformations for each ligand
- Graphs of calculated energies, e.g. binding energy and its components, versus viewed conformers
- Flexible commercial licensing and free for academic use cases
GUI based guided workflow
- User guided step-by-step through system setup, calculation submission, and results analysis
- Load and view target protein and ligands before and after automatic preparation and force field typing
- View docked and ranked ligand conformers and graphed energies/scores
System setup direct from PDB/SDF
- Import protein PDB file, prepare structure, and carry out force field typing
- All atom and united atom protein forcefield typing/parameter assignment available
- Enhanced Dreiding typing/parameter assignment for ligands
Flexible ligand and protein side chains
- Ligand flexibility by allowing ligand torsion angles to change
- User can select protein side chains to have changeable torsion angles introducing receptor mobility
- Option to fully optimize all ligand degrees of freedom after docking
Defining the binding site
- User placement and sizing of box that delimits search region
- If ligand co-crystal or other reference ligand uploaded can center box on it
Analysis of docked ligand conformers
- Display multiple docked conformers for each ligand
- RMSD of docked conformers with reference ligand
- Interrogate ligand conformer interactions/hydrogen bonding with surrounding residues
Ligand ranking and energy analysis
- Ligands can be ranked according various metrics e.g. binding energy, interaction energy, coulomb energy, van der waals etc.
- Screen large ligand sets by off-loading docking to HPC and loading results for analysis
- Use entirely interactively for small to medium ligand sets – fast feedback can help guide early ligand design decisions
Documentation
