Simplified AutoDock force field for hydrated binding sites

Marek Wojciechowski

doi:10.1016/j.jmgm.2017.09.016

Simplified AutoDock force field for hydrated binding sites

Abstract

has been extracted from the Protein Data Bank and used to test and recalibrate AutoDock force field. Since for some binding sites water molecules are crucial for bridging the receptor-ligand interactions, they have to be included in the analysis. To simplify the process of incorporating water molecules into the binding sites and make it less ambiguous, new simple water model was created. After recalibration of the force field on the new dataset much better correlation between the computed and experimentally determined binding affinities was achieved and the quality of pose prediction improved even more

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Marek Wojciechowski dr hab. inż.

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Category:: Articles
Type:: artykuł w czasopiśmie wyróżnionym w JCR
Published in:: JOURNAL OF MOLECULAR GRAPHICS & MODELLING no. 78, pages 74 - 80,
ISSN: 1093-3263
Language:: English
Publication year:: 2017
Bibliographic description:: Wojciechowski M.: Simplified AutoDock force field for hydrated binding sites// JOURNAL OF MOLECULAR GRAPHICS & MODELLING. -Vol. 78, (2017), s.74-80
DOI:: Digital Object Identifier (open in new tab) 10.1016/j.jmgm.2017.09.016
Verified by:: Gdańsk University of Technology