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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
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 practic...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer International Publishing
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028860/ https://www.ncbi.nlm.nih.gov/pubmed/29882064 http://dx.doi.org/10.1007/s10822-018-0123-0 |
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author | Ratamero, Erick Martins Bellini, Dom Dowson, Christopher G. Römer, Rudolf A. |
author_facet | Ratamero, Erick Martins Bellini, Dom Dowson, Christopher G. Römer, Rudolf A. |
author_sort | Ratamero, Erick Martins |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6028860 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Springer International Publishing |
record_format | MEDLINE/PubMed |
spelling | pubmed-60288602018-07-23 Touching proteins with virtual bare hands: Visualizing protein–drug complexes and their dynamics in self-made virtual reality using gaming hardware Ratamero, Erick Martins Bellini, Dom Dowson, Christopher G. Römer, Rudolf A. J Comput Aided Mol Des Article 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. Springer International Publishing 2018-06-07 2018 /pmc/articles/PMC6028860/ /pubmed/29882064 http://dx.doi.org/10.1007/s10822-018-0123-0 Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. |
spellingShingle | Article Ratamero, Erick Martins Bellini, Dom Dowson, Christopher G. Römer, Rudolf A. Touching proteins with virtual bare hands: Visualizing protein–drug complexes and their dynamics in self-made virtual reality using gaming hardware |
title | Touching proteins with virtual bare hands: Visualizing protein–drug complexes and their dynamics in self-made virtual reality using gaming hardware |
title_full | Touching proteins with virtual bare hands: Visualizing protein–drug complexes and their dynamics in self-made virtual reality using gaming hardware |
title_fullStr | Touching proteins with virtual bare hands: Visualizing protein–drug complexes and their dynamics in self-made virtual reality using gaming hardware |
title_full_unstemmed | Touching proteins with virtual bare hands: Visualizing protein–drug complexes and their dynamics in self-made virtual reality using gaming hardware |
title_short | Touching proteins with virtual bare hands: Visualizing protein–drug complexes and their dynamics in self-made virtual reality using gaming hardware |
title_sort | touching proteins with virtual bare hands: visualizing protein–drug complexes and their dynamics in self-made virtual reality using gaming hardware |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028860/ https://www.ncbi.nlm.nih.gov/pubmed/29882064 http://dx.doi.org/10.1007/s10822-018-0123-0 |
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