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Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics

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School of Computing Sciences, University of East Anglia, Norwich, Norfolk NR4 7TJ, United Kingdom
*E-mail: [email protected] (S.H.).
*E-mail: [email protected]. Phone: +44 (0)1603 593542. +44 (0)1603 593795. Fax: +44 (0)1603 593345 (S.D.L.).
Cite this: J. Chem. Inf. Model. 2017, 57, 5, 1142–1152
Publication Date (Web):April 24, 2017
https://doi.org/10.1021/acs.jcim.7b00051
Copyright © 2017 American Chemical Society

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    Abstract

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    Haptic technology facilitates user interaction with the virtual world via the sense of touch. In molecular docking, haptics enables the user to sense the interaction forces during the docking process. Here we describe a haptics-assisted interactive software tool, called Haptimol_RD, for the study of docking interactions. By utilizing GPU-accelerated proximity querying methods very large systems can now be studied. Methods for force scaling, multipoint collision response and haptic navigation are described that address force stability issues that are particular to the interactive docking of large systems. Thus, Haptimol_RD expands, for the first time, the use of interactive biomolecular haptics to the study of protein–protein interactions. Unlike existing approaches, Haptimol_RD is designed to run on relatively inexpensive consumer-level hardware and is freely available to the community.

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    Cited By

    This article is cited by 9 publications.

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    2. Nick Matthews, Akio Kitao, Stephen Laycock, Steven Hayward. Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility. Journal of Chemical Information and Modeling 2019, 59 (6) , 2900-2912. https://doi.org/10.1021/acs.jcim.9b00112
    3. Dean J. Tantillo, Justin B. Siegel, Carla M. Saunders, Teresa A. Palazzo, Phillip P. Painter, Terrence E. O’Brien, Nicole N. Nuñez, Dustin H. Nouri, Michael W. Lodewyk, Brandi M. Hudson, Stephanie R. Hare, Rebecca L. Davis. Computer-Aided Drug Design for Undergraduates. Journal of Chemical Education 2019, 96 (5) , 920-925. https://doi.org/10.1021/acs.jchemed.8b00712
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    5. Georgios Iakovou, Mousa Alhazzazi, Steven Hayward, Stephen D Laycock, . DockIT: a tool for interactive molecular docking and molecular complex construction. Bioinformatics 2021, 36 (24) , 5698-5700. https://doi.org/10.1093/bioinformatics/btaa1059
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    7. Arif Pramudwiatmoko, Satoru Tsutoh, Gregory Gutmann, Yutaka Ueno, Akihiko Konagaya. A high-performance haptic rendering system for virtual reality molecular modeling. Artificial Life and Robotics 2019, 24 (4) , 542-549. https://doi.org/10.1007/s10015-019-00555-9
    8. Torin Adamson, Julian Antolin Camarena, Lydia Tapia, Bruna Jacobson. Optimizing Low Energy Pathways in Receptor-Ligand Binding with Motion Planning. 2019, 2041-2048. https://doi.org/10.1109/BIBM47256.2019.8983169
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