1. Introduction

GriDock was designed to perform the molecular dockings of a large number of ligands stored in a single database (in a format supported by VEGA) in the lowest possible time. It take the full advantage of all local and remote CPUs thanks the MPICH2 technology, balancing the computational load between processors/grid nodes. The docking procedure consists in some steps:

  1. Extraction of the molecule from the database (VEGA command line).
  2. Addition of the hydrogens if they are missing (VEGA command line).
  3. Atomic charges calculation, potential attribution (AMBER), search of the flexible torsion angles and conversion in PDBQT format (VEGA command line).
  4. Molecular docking (AutoDock 4).
  5. Selection of the best scored complex and ranking in the result list.
  6. Storing of the AutoDock output in a compressed Zip archive for a successive analysis (e.g. with VEGA ZZ 2.3.0).

Main features: