Please use this identifier to cite or link to this item: https://doi.org/10.1016/j.bbapap.2012.05.014
Title: Z-score biological significance of binding hot spots of protein interfaces by using crystal packing as the reference state
Authors: Liu, Q.
Wong, L. 
Li, J.
Keywords: Binding hot spots
Crystal packing
Z-score biological significance
Issue Date: 2012
Source: Liu, Q., Wong, L., Li, J. (2012). Z-score biological significance of binding hot spots of protein interfaces by using crystal packing as the reference state. Biochimica et Biophysica Acta - Proteins and Proteomics 1824 (12) : 1457-1467. ScholarBank@NUS Repository. https://doi.org/10.1016/j.bbapap.2012.05.014
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. Crown Copyright © 2012 Published by Elsevier B.V. All rights reserved.
Source Title: Biochimica et Biophysica Acta - Proteins and Proteomics
URI: http://scholarbank.nus.edu.sg/handle/10635/41729
ISSN: 15709639
DOI: 10.1016/j.bbapap.2012.05.014
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