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Bioactive focus in conformational ensembles: a pluralistic approach

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Abstract

Computational generation of conformational ensembles is key to contemporary drug design. Selecting the members of the ensemble that will approximate the conformation most likely to bind to a desired target (the bioactive conformation) is difficult, given that the potential energy usually used to generate and rank the ensemble is a notoriously poor discriminator between bioactive and non-bioactive conformations. In this study an approach to generating a focused ensemble is proposed in which each conformation is assigned multiple rankings based not just on potential energy but also on solvation energy, hydrophobic or hydrophilic interaction energy, radius of gyration, and on a statistical potential derived from Cambridge Structural Database data. The best ranked structures derived from each system are then assembled into a new ensemble that is shown to be better focused on bioactive conformations. This pluralistic approach is tested on ensembles generated by the Molecular Operating Environment’s Low Mode Molecular Dynamics module, and by the Cambridge Crystallographic Data Centre’s conformation generator software.

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  1. Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK

    Matthew Habgood

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  1. Matthew Habgood
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Correspondence to Matthew Habgood.

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Habgood, M. Bioactive focus in conformational ensembles: a pluralistic approach. J Comput Aided Mol Des 31, 1073–1083 (2017). https://doi.org/10.1007/s10822-017-0089-3

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  • DOI: https://doi.org/10.1007/s10822-017-0089-3

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