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Exponential Repulsion Improves Structural Predictability of Molecular Docking
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SYSNO ASEP 0467239 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Exponential Repulsion Improves Structural Predictability of Molecular Docking Author(s) Bazgier, Václav (UEB-Q) ORCID, RID
Berka, K. (CZ)
Otyepka, M. (CZ)
Banáš, P. (CZ)Number of authors 4 Source Title Journal of Computational Chemistry. - : Wiley - ISSN 0192-8651
Roč. 37, č. 28 (2016), s. 2485-2494Number of pages 10 s. Language eng - English Country US - United States Keywords cyclin-dependent kinases ; structure-based design ; scoring functions ; cdk2 inhibitors ; force-field ; ligand interactions ; drug discovery ; purine ; potent ; protein-kinase-2 ; molecular docking ; dock 6.6 ; drug design ; cyclin-dependent kinase 2 ; directory of decoys Subject RIV CF - Physical ; Theoretical Chemistry Institutional support UEB-Q - RVO:61389030 UT WOS 000387484200001 DOI 10.1002/jcc.24473 Annotation Molecular docking is a powerful tool for theoretical prediction of the preferred conformation and orientation of small molecules within protein active sites. The obtained poses can be used for estimation of binding energies, which indicate the inhibition effect of designed inhibitors, and therefore might be used for in silico drug design. However, the evaluation of ligand binding affinity critically depends on successful prediction of the native binding mode. Contemporary docking methods are often based on scoring functions derived from molecular mechanical potentials. In such potentials, nonbonded interactions are typically represented by electrostatic interactions between atom-centered partial charges and standard 6-12 Lennard-Jones potential. Here, we present implementation and testing of a scoring function based on more physically justified exponential repulsion instead of the standard Lennard-Jones potential. We found that this scoring function significantly improved prediction of the native binding modes in proteins bearing narrow active sites such as serine proteases and kinases. Workplace Institute of Experimental Botany Contact David Klier, knihovna@ueb.cas.cz, Tel.: 220 390 469 Year of Publishing 2017
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