Interactive Molecular Dynamics in Virtual Reality (iMD-VR) Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease

Deeks, Helen M.; Walters, Rebecca; Barnoud, Jonathan; Glowacki, David R.; Mulholland, Adrian J.

doi:10.26434/chemrxiv.12834335.v2

Cited by 1 publication

(1 citation statement)

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“…47 In their search for drugs to treat COVID-19, they also used their approach to construct substrate and inhibitor complexes of the key SARS-CoV-2 protein Mpro . 77 These interactive tools have also more generally been flagged as useful for the fight against the pandemic. 186 Finally, we can cite examples of serious games that have been used in research, such as the UDock interactive protein docking system for exploring the possible conformations of protein complexes 167 and the well-known online multiplayer game FoldIt, which aims to engage a wide audience in solving difficult problems such as refining protein structures.…”

Section: Interactive Tools and Applications For Biologymentioning

confidence: 99%

Wielding the power of interactive molecular simulations

Lanrezac

Férey

Baaden

2021

WIREs Comput Mol Sci

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Since the dawn of the computer age, scientists have designed devices to represent molecular structures and developed tools to simulate their dynamic behavior in silico. To this day, these tools remain central to our understanding of biomolecular phenomena. In contrast to other fields such as fluid mechanics or meteorology, the observation of molecular motions at the atomic level remains a major experimental challenge. Continuous advances in computer graphics and numerical computation, combined with the emergence of humancomputer interaction approaches, led to the methodology of so-called "interactive molecular simulations", characterized by two main features. First, the possibility to visualize a running simulation in interactive time, that is, compatible with human perception. Second, the possibility to manipulate the simulation interactively by imposing a force, changing a biophysical property, or editing runtime parameters on the fly. Such simulations are still little used in computational biology, where it is more common to run a series of offline simulations and then visualize and analyze the results. However, interactive molecular simulation tools promise to handle time-consuming tasks such as the modeling of particularly complex biomolecular structures more efficiently or to support approaches such as Rational Drug Design with regard to pharmaceutical applications.

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