VM2 users with access to Chemical Computing Group’s (CCG) Molecular Operating Environment (MOE) graphical interface can now analyze VM2 binding free energy results using a MOE SVL plugin. Download the VM2 MOE plugin from the CCG SVL Exchange.
VM2 3.0 includes an end-to-end workflow capability that automates system setup and forcefield typing/parameter assignment, ligand 2D to 3D conversion, generation of initial receptor-ligand conformations, submission of free energy calculations via resource managers, and collection and organization of final binding free energy results. Extensive benchmarking of VM2 3.0 predicted binding free...
Professor Mike Gilson, co-founder of VeraChem, talks about our VM2 software for fast, accurate calculation of protein-ligand binding free energies, including mining minima theory, implementation, benchmarks, and directions. See Professor Gilson’s presentation here.
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 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.
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 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 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 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 has been awarded a patent for its end-point free-energy method VM2. USPTO 8,140,268
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