Nathan R. Kern

TL;DR: These tools are expected to be useful in innovative and novel glycolipid/LPS/LOS modeling and simulation research by easing tedious and intricate steps in modeling complex biological systems and shall provide insight into structures, dynamics, and underlying mechanisms of complex glycolIPid-/ LPS-/LOS-containing biological membrane systems.

TL;DR: This technical study describes all-atom modeling and simulation of a fully glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane and makes structures available in CHARMM-GUI COVID-19 Archive so that researchers can use these models to carry out innovative and novel modeling andsimulation research for the prevention and treatment of CO VID-19.

TL;DR: A computational tool, Glycan Modeler for in silico N-/O-glycosylation of the target protein and generation of carbohydrate-only systems and the structural properties of modeled glycan structures investigated by running 2-μs molecular dynamics simulations of HIV envelope protein.

TL;DR: The development of FF-Converter is presented to prepare Amber simulation inputs with various Amber force fields within the current CHARMM-GUI workflow to support other simulation programs that support the Amber force field.

TL;DR: In this article, a fully-glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane was modeled using template-based modeling, de-novo protein structure prediction, and loop modeling techniques in GALAXY.