VDock

VDock is VeraChem LLC's fast protein-ligand docking and scoring software package, designed to guide computational chemists and drug discovery researchers through the full docking workflow — from system setup through calculation submission to results analysis. It combines an intuitive graphical user interface with powerful docking algorithms, making it suitable for both interactive use on small to medium ligand sets and large-scale virtual screening campaigns offloaded to high-performance computing (HPC) environments.

VDock is available under flexible commercial licensing terms and is free for academic use cases, making it accessible to a broad range of users across industry and academia.

GUI-Based Guided Workflow

• Intuitive graphical user interface (GUI) serves as the front end to the protein-ligand docking calculation engine.
• Users are guided step-by-step through system setup, calculation submission, and results analysis.
• Target protein and ligands can be loaded and viewed before and after automatic preparation and force field typing.
• Docked and ranked ligand conformers and graphed energies/scores can be visualised directly within the interface.

System Setup Direct from PDB and SDF Files

• Seamless setup and docking directly from import of a raw protein PDB file and a ligand series SD file.
• Protein structure preparation and force field typing are carried out automatically upon import.
• Both all-atom and united-atom protein force field typing and parameter assignment are available.
• Enhanced Dreiding typing and parameter assignment is used for ligands.

Flexible Ligand and Protein Side Chains

• Ligand flexibility is modelled by allowing ligand torsion angles to change during docking.
• Users can select specific protein side chains to have changeable torsion angles, introducing receptor mobility into the docking calculation.
• An option is available to fully optimise all ligand degrees of freedom after the initial docking step.

Defining the Binding Site

• Users can manually place and size a box that delimits the docking search region within the protein.
• A ligand co-crystal structure or other reference ligand can be uploaded to automatically centre the search box on the known binding site.

Search Algorithms

• Multiple search techniques are available, including Global Underestimator Methods, Genetic Algorithms, Poling, and Tabu Search.

Analysis of Docked Ligand Conformers

• Multiple docked conformers for each ligand can be displayed and compared.
• RMSD of docked conformers relative to a reference ligand can be calculated.
• Ligand conformer interactions and hydrogen bonding with surrounding protein residues can be interrogated.
• Post-docking analysis includes visualisation of multiple docked conformations for each ligand.

Ligand Ranking and Energy Analysis

• Ligands can be ranked according to various metrics, including binding energy, interaction energy, Coulomb energy, and van der Waals energy.
• Graphs of calculated energies and their components versus viewed conformers are available for detailed analysis.
• Large ligand sets can be screened by offloading docking calculations to HPC infrastructure, with results loaded back into the GUI for analysis.
• Fully interactive use for small to medium ligand sets provides fast feedback to help guide early ligand design decisions.

VDock is part of VeraChem's broader suite of computational chemistry tools and is supported by comprehensive documentation including a user manual and tutorial. Docking calculations can be run directly on the desktop or exported to HPC environments, providing flexibility to suit different project scales and infrastructure setups.