Products

VM2

VM2 is VeraChem's newest software package. Based upon a rigorous statistical thermodynamics framework, VM2 can provide accurate protein-ligand and host-guest binding free energies. It treats binding sites and ligands as fully flexible. A combination of rigorous conformational search algorithms with an energy model that includes solvation and entropic terms, make VM2 the most advanced end-point free energy method in routine use today. The latest version of VM2 is parallel processor enabled (MPI, OpenMP, CUDA).

VCharge

VCharge reliably and rapidly provides partial atomic charges for drug-like molecules. This application accurately reproduces charges determined by ab initio electrostatic potential calculations. Taking less than 0.1 seconds/compound VCharge is a fast alternative to the commonly used AM1/BCC. The application reads and writes SD files and results can be conveniently reviewed by VeraChem's freely available VDisplay. VCharge is currently available as a command-line driven Linux or MS Windows application.

VConf

VConf is a user friendly, but powerful application that provides low-energy conformations of drug-like molecules. Given a 2D or 3D SD file of compounds, VConf rapidly constructs multiple starting structures and explores their potential energy surfaces through VeraChem's unique TORK algorithm. The search procedure is both symmetry and parity aware. It is suitable for application to single molecules or databases of drug-like molecules, and is currently available as a command-line driven Linux or MS Windows application.

VFilter

Given multiple conformations of the same molecule, VeraChem's VFilter application determines if any are duplicates within user-specified tolerances, and any duplicates found are removed. VFilter is algorithmically aware of global and local molecular symmetry, so it can recognize as identical structures in which, for example, a ring may be rotated 180 degrees. The application reads and writes SD files, and a command-line driven Linux version and an MS Windows version, with a graphical user interface, are available.

Vrms

Vrms calculates the symmetry-corrected root-mean-square deviation (RMSD) between a reference molecular conformation and a series of conformations of the same molecule. For small drug-like molecules alone, Vrms carries out a molecular superposition procedure that accounts for global and local symmetry; for drug-like molecules docked to protein targets, no superposition is carried out. The application reads and writes SD files, and a command-line driven Linux version and an MS Windows version, with a graphical user interface, are available.

VDisplay

VDisplay is a freely available 3D molecular viewer. It reads SD files and can be used to conveniently visualize results from VeraChem's small molecule applications: VCharge, VConf, VFilter, and Vrms. The user can step through or jump to particular molecular conformations. Vdisplay is currently available as a MS Windows application.