Molecular Surface Representation Using 3D Zernike Descriptors for Protein Shape Comparison and Docking

Author(s): Daisuke Kihara, Lee Sael, Rayan Chikhi, Juan Esquivel-Rodriguez.

Journal Name: Current Protein & Peptide Science

Volume 12 , Issue 6 , 2011

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Abstract:

The tertiary structures of proteins have been solved in an increasing pace in recent years. To capitalize the enormous efforts paid for accumulating the structure data, efficient and effective computational methods need to be developed for comparing, searching, and investigating interactions of protein structures. We introduce the 3D Zernike descriptor (3DZD), an emerging technique to describe molecular surfaces. The 3DZD is a series expansion of mathematical three-dimensional function, and thus a tertiary structure is represented compactly by a vector of coefficients of terms in the series. A strong advantage of the 3DZD is that it is invariant to rotation of target object to be represented. These two characteristics of the 3DZD allow rapid comparison of surface shapes, which is sufficient for real-time structure database screening. In this article, we review various applications of the 3DZD, which have been recently proposed.

Keywords: 3D Zernike descriptor, protein surface comparison, ligand binding site comparison, protein docking prediction, tertiary structure, computational methods, protein structures, 3DZD, grid points, 3D function

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Article Details

VOLUME: 12
ISSUE: 6
Year: 2011
Page: [520 - 530]
Pages: 11
DOI: 10.2174/138920311796957612
Price: $58

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