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AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis

Greener, JG; Sternberg, MJE; (2015) AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis. BMC Bioinformatics , 16 (1) , Article 335. 10.1186/s12859-015-0771-1. Green open access

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Abstract

BACKGROUND: Despite being hugely important in biological processes, allostery is poorly understood and no universal mechanism has been discovered. Allosteric drugs are a largely unexplored prospect with many potential advantages over orthosteric drugs. Computational methods to predict allosteric sites on proteins are needed to aid the discovery of allosteric drugs, as well as to advance our fundamental understanding of allostery. RESULTS: AlloPred, a novel method to predict allosteric pockets on proteins, was developed. AlloPred uses perturbation of normal modes alongside pocket descriptors in a machine learning approach that ranks the pockets on a protein. AlloPred ranked an allosteric pocket top for 23 out of 40 known allosteric proteins, showing comparable and complementary performance to two existing methods. In 28 of 40 cases an allosteric pocket was ranked first or second. The AlloPred web server, freely available at http://www.sbg.bio.ic.ac.uk/allopred/home, allows visualisation and analysis of predictions. The source code and dataset information are also available from this site. CONCLUSIONS: Perturbation of normal modes can enhance our ability to predict allosteric sites on proteins. Computational methods such as AlloPred assist drug discovery efforts by suggesting sites on proteins for further experimental study.

Type: Article
Title: AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/s12859-015-0771-1
Publisher version: https://doi.org/10.1186/s12859-015-0771-1
Language: English
Additional information: © Greener and Sternberg 2015. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/).
Keywords: Allostery, Normal modes, Pocket prediction, Machine learning, Web server
UCL classification: UCL
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Computer Science
URI: https://discovery.ucl.ac.uk/id/eprint/10074643
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