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by morris last modified 2014-12-08 12:32

Here are some Tools and Databases that will be useful in docking.

Science AutoDockTools Hydrated Docking AutoDockZN forcefield Raccoon Raccoon2 Fox AutoLigand Parameters Tools Databases Scripts Movies

AutoDock Set-up and Analysis

  • ADT / AutoDockTools — designed for AutoDock and AutoGrid. It is built on Michel Sanner's PMV, and is available in two forms:
      • prepare the ligand input PDBQ and PDBQT files for AutoDock
      • prepare the receptor input PDBQS and PDBQT files for AutoGrid
      • create grid parameter files (GPF) to set up AutoGrid calculations
      • create docking parameter files (DPF) for AutoDock calculations
      • analyse the docking results from AutoDock log files (DLG)
      • isocontour AutoGrid maps to assist in understanding ligand binding and in designing more potent inhibitors
  • BDT — ("Blind Docking Tool") third-party GUI software that can:
    • combine AutoGrid maps for different sctructures, to account for flexibility in the receptor
    • make staggered non-overlapping sets of AutoGrid maps, to cover a very large receptor when performing blind docking
    • help to set up AutoDock input files for virtual screening of a library of molecules against one or more receptors

Hydrogens, Hydrogen-Bond Networks and Waters

    • predicts & optimizes the positions and orientations of internal, buried water molecules
    • automatically adds polar hydrogens are ed to the structure
    • extended to work with DNA by Andy McCammon's Group member Cameron Mura
    • constructs "an atomic solvent environment model for a given atomic macromolecule model for use in molecular dynamics simulations", and can place salt ions, and buried waters, too.
  • * HBPLUS
    • is a hydrogen bond calculation program "calculates hydrogen positions, deals with hydrogens that can occupy more than one position; optionaly includes amino-aromatic H-bonds" and "analyses H-bonding Near Asn, Gln and His Side-Chains and suggests optimal conformations".



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