Comparing the mechanical properties of SARS-CoV-1 spike protein with that of SARS-CoV-2 spike protein, we were able to determine the mutations that were key in the elevated mechanical stability of the proteins of the COVID-19 outbreak compared to that of the early 2000s outbreak.
Dynamical Network Analysis can be used to identify important residues and information pathways within molecular complexes. The package described in this work allows users to analyze MD trajectories and produce high-quality biomolecular images.
Bacterial colonization of the human intestine requires firm adhesion of bacteria to insoluble substrates under hydrodynamic flow. Here we report the molecular mechanism behind an ultrastable protein complex responsible for resisting shear forces in the human gut.
NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. In this new reference paper for NAMD, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance.
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