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J Mol Graph Model. 2011 Nov;31:5-9. doi: 10.1016/j.jmgm.2011.07.008. Epub 2011 Aug 7.

HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis.

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1
Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093-0365, United States. jdurrant@ucsd.edu

Abstract

In the current work, we present a hydrogen-bond analysis of 2673 ligand-receptor complexes that suggests the total number of hydrogen bonds formed between a ligand and its receptor is a poor predictor of ligand potency; furthermore, even that poor prediction does not suggest a statistically significant correlation between hydrogen-bond formation and potency. While we are not the first to suggest that hydrogen bonds on average do not generally contribute to ligand binding affinities, this additional evidence is nevertheless interesting. The primary role of hydrogen bonds may instead be to ensure specificity, to correctly position the ligand within the active site, and to hold the protein active site in a ligand-friendly conformation. We also present a new computer program called HBonanza (hydrogen-bond analyzer) that aids the analysis and visualization of hydrogen-bond networks. HBonanza, which can be used to analyze single structures or the many structures of a molecular dynamics trajectory, is open source and python implemented, making it easily editable, customizable, and platform independent. Unlike many other freely available hydrogen-bond analysis tools, HBonanza provides not only a text-based table describing the hydrogen-bond network, but also a Tcl script to facilitate visualization in VMD, a popular molecular visualization program. Visualization in other programs is also possible. A copy of HBonanza can be obtained free of charge from http://www.nbcr.net/hbonanza.

PMID:
21880522
PMCID:
PMC3218086
DOI:
10.1016/j.jmgm.2011.07.008
[Indexed for MEDLINE]
Free PMC Article
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