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J Comput Aided Mol Des. 2018 Jun;32(6):703-709. doi: 10.1007/s10822-018-0123-0. Epub 2018 Jun 7.

Touching proteins with virtual bare hands : Visualizing protein-drug complexes and their dynamics in self-made virtual reality using gaming hardware.

Author information

1
Department of Physics and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
2
School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
3
Department of Physics, University of Warwick, Coventry, CV4 7AL, UK. r.roemer@warwick.ac.uk.

Abstract

The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal chemists while attempting the above to access the information contained in three-dimensional structures by using two-dimensional projections, which can preclude disclosure of useful features. A more accessible and intuitive visualization of the three-dimensional configuration of the atomic geometry in the models can be achieved through the implementation of immersive virtual reality (VR). While bespoke commercial VR suites are available, in this work, we present a freely available software pipeline for visualising protein structures through VR. New consumer hardware, such as the HTC VIVE and the OCULUS RIFT utilized in this study, are available at reasonable prices. As an instructive example, we have combined VR visualization with fast algorithms for simulating intramolecular motions of protein flexibility, in an effort to further improve structure-led drug design by exposing molecular interactions that might be hidden in the less informative static models. This is a paradigmatic test case scenario for many similar applications in computer-aided molecular studies and design.

KEYWORDS:

Anti-microbial resistance; Molecular design; Protein dynamics; Virtual reality

PMID:
29882064
PMCID:
PMC6028860
DOI:
10.1007/s10822-018-0123-0
[Indexed for MEDLINE]
Free PMC Article

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