An improved convex and concave index for revealing the exposure degree of atoms in protein 3D structure Online publication date: Fri, 24-Nov-2017
by Xiao Wang; Jian Zhao; Yujiao Yan; Jingye Qian; Ping Han; Xiaofeng Song
International Journal of Computational Biology and Drug Design (IJCBDD), Vol. 10, No. 4, 2017
Abstract: Geometric property of protein surface contributes largely to the protein function in the cells, and descriptors of measuring the convexity and concavity of protein surfaces can help understand the protein function. Motivated by CX algorithm, we developed an improved surface structural parameter named convex-and-concave index (CCI) to describe geometric properties of protein surface. The proposed CCI eliminates the defect of coarse computing for the overlap volume of two adjacent atom spheres in CX algorithm, by dividing the probe sphere into many cubic lattices and labelling the cubic lattices inside the atoms or not, respectively. The results indicated that the CCI algorithm improved the accuracy of CX, and not increased the computing complexity. The proposed CCI is a fast and simple method that can accurately describe the exposure degree of atoms in protein and reveal protein functional sites, such as active sites and ubiquitination sites.
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