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Touching proteins with virtual bare hands : visualizing protein–drug complexes and their dynamics in self-made virtual reality using gaming hardware
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Ratamero, Erick Martins, Bellini, Dom, Dowson, Christopher G. and Römer, Rudolf A. (2018) Touching proteins with virtual bare hands : visualizing protein–drug complexes and their dynamics in self-made virtual reality using gaming hardware. Journal of Computer-Aided Molecular Design, 32 (6). pp. 703-709. doi:10.1007/s10822-018-0123-0 ISSN 1573-4951.
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WRAP-touching-proteins-virtual-bare-hands-Roemer-2018.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (2167Kb) | Preview |
Official URL: http://dx.doi.org/10.1007/s10822-018-0123-0
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.
| Item Type: | Journal Article | ||||||||
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| Subjects: | R Medicine > RS Pharmacy and materia medica | ||||||||
| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) Faculty of Science, Engineering and Medicine > Science > Physics |
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| Library of Congress Subject Headings (LCSH): | Drugs -- Design -- Molecular aspects -- Software, Proteins | ||||||||
| Journal or Publication Title: | Journal of Computer-Aided Molecular Design | ||||||||
| Publisher: | Springer | ||||||||
| ISSN: | 1573-4951 | ||||||||
| Official Date: | 7 June 2018 | ||||||||
| Dates: |
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| Volume: | 32 | ||||||||
| Number: | 6 | ||||||||
| Page Range: | pp. 703-709 | ||||||||
| DOI: | 10.1007/s10822-018-0123-0 | ||||||||
| Status: | Peer Reviewed | ||||||||
| Publication Status: | Published | ||||||||
| Access rights to Published version: | Open Access (Creative Commons) | ||||||||
| Date of first compliant deposit: | 18 June 2018 | ||||||||
| Date of first compliant Open Access: | 18 June 2018 | ||||||||
| RIOXX Funder/Project Grant: |
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