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Comput Biol Chem. 2013 Dec;47:16-23. doi: 10.1016/j.compbiolchem.2013.06.003. Epub 2013 Jun 25.

Computational structure analysis of biomacromolecule complexes by interface geometry.

Author information

1
Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; Laboratory of Algorithms and Computational Geometry, Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran. Electronic address: s_mahdavi@aut.ac.ir.

Abstract

The ability to analyze and compare protein-nucleic acid and protein-protein interaction interface has critical importance in understanding the biological function and essential processes occurring in the cells. Since high-resolution three-dimensional (3D) structures of biomacromolecule complexes are available, computational characterizing of the interface geometry become an important research topic in the field of molecular biology. In this study, the interfaces of a set of 180 protein-nucleic acid and protein-protein complexes are computed to understand the principles of their interactions. The weighted Voronoi diagram of the atoms and the Alpha complex has provided an accurate description of the interface atoms. Our method is implemented in the presence and absence of water molecules. A comparison among the three types of interaction interfaces show that RNA-protein complexes have the largest size of an interface. The results show a high correlation coefficient between our method and the PISA server in the presence and absence of water molecules in the Voronoi model and the traditional model based on solvent accessibility and the high validation parameters in comparison to the classical model.

KEYWORDS:

Alpha complex; Computational geometry; Protein–nucleic acid complexes; Protein–protein complexes; Voronoi diagram

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