Posts by Simon Webb

A joint VeraChem, Iowa State University, and University of Colorado Denver study applying QM-VM2 to the calculation of host-guest binding free energies published in the Journal of Chemical Physics.

QM-VM2, which efficiently combines statistical mechanics with quantum mechanical (QM) energy potentials in order to calculate noncovalent binding free energies of host–guest systems, is presented. QM-VM2 efficiently couples the use of semi-empirical QM (SEQM) energies and geometry optimizations with an underlying molecular mechanics (MM) based conformational search, to find low...

VeraChem’s newly developed CloudVM2 capability applied in early stage R&D efforts

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 multi-GPU 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

VeraChem’s development team present the VM2 protein-ligand binding free energy method at Janssen Pharmaceutical

VeraChem’s development team carry out a presentation of the VM2 protein-ligand binding free energy method at Janssen Pharmaceutical, and make agreement for trial usage of the VM2 software package.

VeraChem’s development team carry out presentation of the VM2 protein-ligand binding free energy method at Dart NeuroScience

VeraChem’s development team carry out a presentation of the VM2 protein-ligand binding free energy method at Dart NeuroScience LLC, and make agreement for trial usage of the VM2 software package.

VeraChem awarded patent for its end-point binding free energy method VM2

VeraChem awarded patent for its end-point binding free energy method VM2

VeraChem has been awarded a patent for its end-point free-energy method VM2.  USPTO 8,140,268

Virtual screening application ReverseScreen3D using VeraChem’s VConf for generation of 3D ligand conformations

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...

Protein-ligand homology modeling web application using VeraChem’s VCharge and VConf packages

Protein-ligand homology modeling web application using VeraChem’s VCharge and VConf packages

The recently available web based protein-ligand homology modeling application SitesModel developed at the University of Leeds uses VeraChem’s VCharge to generate ligand partial atomic charges and VConf to generate ligand 3D conformations.

PreADMET 2.0 software package developer provides interface to VeraChem’s VConf package

PreADMET 2.0 software package developer provides interface to VeraChem’s VConf package

The PreADMET 2.0 commercial software package for absorption – distribution – metabolism – excretion – toxicity (ADMET) prediction now provides an interface to VeraChem’s 3D ligand conformational search package VConf.