Z-score biological significance of binding hot spots of protein interfaces by using crystal packing as the reference state

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dc.contributor.author Liu, Qian en_US
dc.contributor.author Wong, Limsoon en_US
dc.contributor.author Li, Jinyan en_US
dc.contributor.editor en_US
dc.date.accessioned 2014-04-03T01:23:42Z
dc.date.available 2014-04-03T01:23:42Z
dc.date.issued 2012 en_US
dc.identifier 2012001036 en_US
dc.identifier.citation Liu, Qian, Wong, Limsoon, and Li, Jinyan 2012, 'Z-score biological significance of binding hot spots of protein interfaces by using crystal packing as the reference state', BBA - Proteins and Proteomics, vol. 1824, no. 12, pp. 1457 en_US
dc.identifier.issn 1570-9639 en_US
dc.identifier.other C1 en_US
dc.identifier.uri http://hdl.handle.net/10453/23089
dc.description.abstract Characterization of binding hot spots of protein interfaces is a fundamental study in molecular biology. Many computational methods have been proposed to identify binding hot spots. However, there are few studies to assess the biological significance of binding hot spots. We introduce the notion of biological significance of a contact residue for capturing the probability of the residue occurring in or contributing to protein binding interfaces. We take a statistical Z-score approach to the assessment of the biological significance. The method has three main steps. First, the potential score of a residue is defined by using a knowledge-based potential function with relative accessible surface area calculations. A null distribution of this potential score is then generated from artifact crystal packing contacts. Finally, the Z-score significance of a contact residue with a specific potential score is determined according to this null distribution. We hypothesize that residues at binding hot spots have big absolute values of Z-score as they contribute greatly to binding free energy. Thus, we propose to use Z-score to predict whether a contact residue is a hot spot residue. Comparison with previously reported methods on two benchmark datasets shows that this Z-score method is mostly superior to earlier methods. This article is part of a Special Issue entitled: Computational Methods for Protein Interaction and Structural Prediction. en_US
dc.language en_US
dc.publisher Elsevier en_US
dc.relation.isbasedon http://dx.doi.org/10.1016/j.bbapap.2012.05.014 en_US
dc.title Z-score biological significance of binding hot spots of protein interfaces by using crystal packing as the reference state en_US
dc.parent BBA - Proteins and Proteomics en_US
dc.journal.volume 1824 en_US
dc.journal.number 12 en_US
dc.publocation The Netherland en_US
dc.identifier.startpage 1457 en_US
dc.identifier.endpage en_US
dc.identifier.endpage 1467 en_US
dc.cauo.name FEIT.A/DRsch Ctr Quantum Computat'n & Intelligent Systs en_US
dc.conference Verified OK en_US
dc.for 090300 en_US
dc.personcode 0000061977 en_US
dc.personcode 114466 en_US
dc.personcode 112261 en_US
dc.percentage 100 en_US
dc.classification.name Biomedical Engineering en_US
dc.classification.type FOR-08 en_US
dc.edition en_US
dc.custom en_US
dc.date.activity en_US
dc.location.activity en_US
dc.description.keywords Binding hot spots; Crystal packing; Z-score biological significance en_US
dc.staffid 112261 en_US

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