VeraChem, LLC software

Superimpose related ligand series on reference structure Reference can be co-xtal PDB, sdf, mol, crd Handles arbitrary atom orderings. Provides excellent VM2/docking starting structures. 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.

VFilter analyzes multiple conformations of a molecule and removes conformations that are identical to within user-specified tolerances. Both global and local chemical symmetries are accounted for when comparing a pair of conformations. For example, if two conformations differ only by a 180º rotation of a benzene ring, the local symmetry of the benzene is detected and applied so that the two conformations are recognized as identical. Alternate resonance forms, but not tautomers, are also accounted for when identifying symmetries. Analyzes ensembles of molecular conformations and removes repeats Takes into account local and global molecular symmetries Symmetry detection recognizes resonance forms.

VDisplay is a freely available 3D molecular viewer which reads the SDfiles produced by VCharge and VConf provides an easy, graphical way to view the results on a Windows computer. VDisplay can also read and display SDfiles produced by other programs. VDisplay allows the user to step through molecules in the SDfile one by one, or jump to a specific molecule via a simple name search. A range of other display controls support rotation, translation, scaling, coloring, recentering, full-screen display, menu tear-offs, etc.