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

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

Volume: 12 Issue: 6

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

Affiliation:

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

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.

Cite this article as:

Kihara Daisuke, Sael Lee, Chikhi Rayan and Esquivel-Rodriguez Juan, Molecular Surface Representation Using 3D Zernike Descriptors for Protein Shape Comparison and Docking, Current Protein & Peptide Science 2011; 12 (6) . https://dx.doi.org/10.2174/138920311796957612