VeraChem has developed a capability to run its protein-ligand binding free energy software package on the Amazon Web Services cloud environment. This CloudVM2 package enables calculation of protein-ligand binding affinities for hundreds of ligands per day, and was recently applied in early stage R&D efforts by Sarfez Pharmaceuticals Inc.
Pfizer now using VeraChem’s MPI+CUDA enabled version of its VM2 protein-ligand binding free energy software package
VeraChem’s VM2 package has been ported for running on multiple GPUs using a hybrid MPI+CUDA approach. This highly accelerated version of VM2 is now in use by computational chemists at Pfizer.
VeraChem’s protein-ligand binding free energy software VM2 used in study of ligand binding to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT)
VeraChem’s protein-ligand binding free energy software VM2 used in the study “Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design”, PLoS Comput Biol 12(8): e1005057. DOI:10.1371/journal.pcbi.1005057
Invited presentation titled “VM2 Methodology and Software for Calculation of Binding Free Energies: Application to Protein-Ligand and Host-Guest Systems” given by Dr. Simon Webb at the Advanced Biomedical Computing Center, SAIC-Frederick.
VeraChem’s software now licensed to over 500 academic researchers worldwide.
VeraChem’s protein-ligand binding affinity prediction software package VM2 applied to the study of p38a MAP kinase. “Insights from Free-Energy Calculations: Protein Conformational Equilibrium, Driving Forces, and Ligand-Binding Modes”, Biophysical Journal 103(2): 342-351. DOI: 10.1016/j.bpj.2012.05.046
Virtual screening application ReverseScreen3D using VeraChem’s VConf for generation of 3D ligand conformations
Prof. Richard Jackson’s group at the University of Leeds has released a Web based virtual screening application ReverseScreen3D, which uses VeraChem’s VConf package for 3D ligand conformer generation: “Vconf (v2.0 from VeraChem), which uses a stochastic method for conformer searching, was chosen because it has been shown to be highly effective at reproducing bioactive conformations.” Kinnings, S. L. and R. M. Jackson (2011). “ReverseScreen3D: A Structure-Based Ligand Matching Method To identify Protein Targets. “Journal of Chemical Information and Modeling 51(3): 624-634. DOI: 10.1021/ci1003174