iMD-VR to study COVID proteins

Excited about the publication of a recent paper showing how our open source interactive molecular dynamics in virtual reality (iMD-VR) program Narupa can be used to investigate proteins which are relevant to the ongoing COVID pandemic. In the paper, we looked at the main protease (Mpro) of the SARS-CoV-2 virus, which is one focus of drug development efforts for COVID-19. The paper shows that iMD-VR offers a useful and effective tool for creating Mpro complexes in a physically rigorous and flexible way. Applying the iMD-VR approach to both an Mpro inhibitor and an oligopeptide substrate, we show that iMD-VR gives models in agreement with experimentally observed (crystal) structures. The docked structures were tested in MD simulations and found to be stable.

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