The virtual screening front-end for AutoDock 4

PGH2 synthase I - ibuprofen complex

GriDock was designed to perform the molecular dockings of a large number of ligands stored in a single database (SDF or Zip format) in the lowest possible time. It take the full advantage of all local and remote CPUs through 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. Conversion from 2D to 3D (if required) provided by AMMP VE.
  4. Optional structure filter based on the chemical/physical properties calculated by VEGA.
  5. Atomic charges calculation, potential attribution (AMBER), search of the flexible torsion angles and conversion to PDBQT format (VEGA command line).
  6. Molecular docking (AutoDock 4).
  7. Selection of the best scored complex and ranking in the result list.
  8. Storing of the AutoDock output in a compressed Zip archive for a successive analysis (e.g. with VEGA ZZ).

Main features:

Software requirements:

System requirements:

GriDock is included in VEGA ZZ for Windows and VEGA 3.0 for Linux x86-x64-ARM packages.

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