Understanding how proteins interact with membrane surfaces is important for drug discovery studies in which a drug may target a membrane protein. One of the main proteins of interest for COVID-19 antibodies is the ACE2 protein that binds to the neutral amino acid transporter B0AT1. B0AT1 sits in the membrane and understanding how movement or perturbation of that membrane might after the binding sites available on the ACE2 protein is important in creating effective antibodies to prevent viral infection. To study the dynamics associated with membranes, LLNL scientists created MemSurfer. MemSurfer is an efficient and versatile tool to compute and analyze membrane surfaces found in a wide variety of large-scale molecular simulations. MemSurfer works independent of the type of simulation, directly on the 3D point coordinates, and can handle a variety of membranes as well as atomic simulations. MemSurfer provides many in-built analysis tasks, such as computing the membrane curvature, density and normals of lipids, and area per lipid. More importantly, MemSurfer provides a simple-to-use Python API that may be easily used/extended to perform other types of analysis. To get a complete picture associated with COVID-19 antivirals, computational studies should investigate the involvement of the membrane and MemSurfer can be used for those computational analyses.
MemSurfer, open-sourced software licensed under the GPL-3.0 license (LLNL internal case # CP02099)