VMap is an  application to superimpose related ligands (e.g. common scaffold atoms; different R-groups) on a reference molecule. The reference can be, for example, a co-crystalized ligand taken from a protein PDB file, in which case, VMap provides excellent starting structures for VM2 or docking calculations.

  • Superimpose congeneric ligand series on a reference structure
    Identifies the maximum common substructure (MCS) shared by the reference molecule and each of a series of ligands. This information is then used to superimpose each ligand in the series on the reference molecule, maximizing overlap by dihedral rotations.
  • Multiple formats supported
    Reference format can be PDB (e.g. co-xtal ligand), SDF, MOL, or CRD. Ligand series supplied as SDF.
  • Handles arbitrary atom numbering/ordering
    Equivalent atoms mapped automatically – no atom reordering required.
  • 1-Click interface with VDisplay molecular visualization of results
    Send superimposed structures to Verachem’s  VDisplay. Output of atom mappings of the maximum common substructures in a CSV file.

User Options

The VMap graphical user interface provides detailed user control, including:

  • can select molecule is reference from a multi-molecule file
  • if all-atom reference choose wether to include hydrogen atoms in mapping all atom or just heavy-atoms

  • choose whether RMSD calculation includes hydrogen atoms or just heavy atoms
  • choose from rigid superposition or overlap maximization via dihedral rotations

Windows VMap

VMap seamlessly interfaces with VDisplay to visualize the superimposed molecular structures produced.

Vmap version 0.9 for Microsoft Windows®.