Info

Given its relevance, we have tested gmx_MMPBSA with multiple COVID-19 related systems. The ultimate goal is to provide a useful tool for those researchers working on COVID-19 projects. The capability of gmx_MMPBSA to handle systems that combine a number of characteristics (i.e. metalloprotein-ligand, Protein-protein, Membrane proteins, glycosylated proteins etc.) constitutes a tremendous help for those researchers that use MD simulations and binding free energy calculations in their projects. We plan to incorporate more systems as they arise in the literature and databases.

All these systems haven been previously prepared in CHARMM-GUI, and they are available at the CHARMM-GUI Archive - COVID-19 Proteins Library.

References¶

S. Jo, T. Kim, V.G. Iyer, and W. Im (2008) CHARMM-GUI: A Web-based Graphical User Interface for CHARMM. J. Comput. Chem. 29:1859-1865

H. Woo, S-J. Park, Y.K. Choi, T. Park, M. Tanveer, Y. Cao, N.R. Kern, J. Lee, M.S. Yeom, T.I. Croll, C. Seok, and W. Im (2020) Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane. J. Phys. Chem. B. 124:7128–7137

Y.K. Choi, Y. Cao, M. Frank, H. Woo, S-J. Park, M.S. Yeom, T.I. Croll, C. Seok, W. Im (2021) Structure, Dynamics, Receptor Binding, and Antibody Binding of Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane. J. Chem. Theory Comput. (in press)