Hydrogen Bonds in Protein-Ligand Complexes

Fast and reliable evaluation of the hydrogen bond potential energy has a significant impact in the drug design and development since it allows the assessment of large databases of organic molecules in virtual screening projects focused on a protein of interest. Semi-empirical force fields implemente...

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Bibliographic Details
Published inMethods in molecular biology (Clifton, N.J.) Vol. 2053; p. 93
Main Authors Bitencourt-Ferreira, Gabriela, Veit-Acosta, Martina, de Azevedo, Jr, Walter Filgueira
Format Journal Article
LanguageEnglish
Published United States 01.01.2019
Subjects
Molecular recognition
Shikimate pathway
Drug design
Binding affinity
Hydrogen bond interactions
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Summary:Fast and reliable evaluation of the hydrogen bond potential energy has a significant impact in the drug design and development since it allows the assessment of large databases of organic molecules in virtual screening projects focused on a protein of interest. Semi-empirical force fields implemented in molecular docking programs make it possible the evaluation of protein-ligand binding affinity where the hydrogen bond potential is a common term used in the calculation. In this chapter, we describe the concepts behind the programs used to predict hydrogen bond potential energy employing semi-empirical force fields as the ones available in the programs AMBER, AutoDock4, TreeDock, and ReplicOpter. We described here the 12-10 potential and applied it to evaluate the binding affinity for an ensemble of crystallographic structures for which experimental data about binding affinity are available.
ISSN:1940-6029
DOI:10.1007/978-1-4939-9752-7_7