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Haptic-driven, interactive drug design: implementing a GPU-based approach to evaluate the induced fit effect

Anthopoulos, Athanasios, Pasqualetto, Gaia, Grimstead, Ian John and Brancale, Andrea 2014. Haptic-driven, interactive drug design: implementing a GPU-based approach to evaluate the induced fit effect. Faraday Discussions 169 , pp. 323-342. 10.1039/C3FD00139C

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Abstract

In this paper, we describe a hybrid meta-heuristics method of energy minimization and conformational sampling and its application into our haptic-driven molecular modelling simulator. The proposed method has been designed to suit real-time molecular docking simulations, where the time-lapse between two successive ligand poses is relatively small. In these situations, the energy minimization problem becomes increasingly complex and chaotic. The algorithm is tuned to take advantage of recent advances in GPU computing with asynchronous kernel execution, which has allowed us to include full protein flexibility in the real-time interactive, haptic-driven simulations. Finally, in this paper, we will also discuss the implementation of such high-performance computing approaches in our software, discussing the results of our initial validation studies, highlighting the advantages and limitations of such interactive methodology.

Item Type: Article
Date Type: Published Online
Status: Published
Schools: Information Services
Pharmacy
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
R Medicine > RM Therapeutics. Pharmacology
Publisher: Royal Society of Chemistry
ISSN: 1359-6640
Date of First Compliant Deposit: 30 March 2016
Date of Acceptance: 13 March 2014
Last Modified: 28 Jun 2019 18:40
URI: http://orca-mwe.cf.ac.uk/id/eprint/69382

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