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A Structural Comparison Approach for Identifying Small Variations in Binding Sites of Homologous Proteins

Journal article
Authors Ivana Uzelac
Thomas Olsson
Leif A Eriksson
Johan Gottfries
Published in Computational Molecular Bioscience
Volume 5
Issue 3
Pages 45-55
ISSN 2165-3453
Publication year 2015
Published at Department of Chemistry and Molecular Biology
Pages 45-55
Language en
Keywords Protein Comparison, Coagulation Factor, Serine Protease, Binding Site, PCA, OPLS-DA
Subject categories Chemical Sciences


A method for analyzing the protein site similarity was devised aiming at understanding selectivity of homologous proteins and guiding the design of new drugs. The method is based on calculating Cα distances between selected pocket residues and subsequent analysis by multivariate methods. Five closely related serine proteases, the coagulation factors II, VII, IX, X, and XI, were studied and their pocket similarity was illustrated by PCA clustering. OPLS-DA was then applied to identify the residues responsible for the variation. By combining these two multivariate methods, we could successfully cluster the different proteases according to class and identify the important residues responsible for the observed variation.

Page Manager: Webmaster|Last update: 9/11/2012

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