Automated refinement protocol to improve the quality of protein structures deposited in the protein data bank, applied to SARS-Cov-2

Abstract

The COVID-19 pandemic caused by SARS-CoV-2 is a global health emergency. In order to better understand the complications associated with COVID-19, it is critical that research and development teams have access to high-accuracy viral protein structures. Current COVID-19 proteins available on the Protein Data Bank (PDB) contain some moderate- to low-resolution structures. In order to improve the quality of the structures, we use an automated protocol that combines torsional optimization with real-space refinement against the electron density derived from the experimental x-ray data.