VeraChem, LLC software

A comprehensive free energy software package for computer-aided drug discovery and molecular design.

Fast protein-ligand docking and scoring software package with user friendly graphical interface

VConf is a powerful and flexible conformational search application which processes an SD file of drug-like compounds containing an initial 2D or 3D conformation of each molecule. It provides for two major modes of operation:

VDraw is an intuitive 2D chemical drawing application. It has a wide range of templates, which simplifies the drawing of  complex molecules. VDraw also supports the loading of an SD file and editing a previously generated chemical structure. VDraw 2D structures can, with a single click, be sent to Vconf for 2D to 3D conversion and conformational searching.

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.

VCharge provides fast, easy access to accurate partial charges for virtually any drug-like compound. It is thus valuable in a wide range of modeling and QSAR applications. VCharge is available for Linux and Microsoft Windows. A convenient Windows viewer VDisplay is available for free download along with VCharge.  Easy access to fast, accurate partial atomic charges of drug-like molecules Valuable in a wide range of of modeling and QSAR applications.

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.

Vrms provides the symmetry-corrected root-mean-square deviation (RMSD) between a series of test conformations of a drug-like molecule and a reference conformation. Two modes of operation are available.

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.