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