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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...

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Detalles Bibliográficos
Autores principales: Ratamero, Erick Martins, Bellini, Dom, Dowson, Christopher G., Römer, Rudolf A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2018
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.
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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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