Skeleton-based shape analysis of protein models

Zhong Li; Shengwei Qin; Zeyun Yu; Yao Jin

doi:10.1016/j.jmgm.2014.06.012

Skeleton-based shape analysis of protein models

J Mol Graph Model. 2014 Sep:53:72-81. doi: 10.1016/j.jmgm.2014.06.012. Epub 2014 Jul 12.

Authors

Zhong Li¹, Shengwei Qin², Zeyun Yu³, Yao Jin²

Affiliations

¹ College of Science, Zhejiang Sci-Tech University, Hangzhou 310018, China. Electronic address: lizhong@zstu.edu.cn.
² College of Science, Zhejiang Sci-Tech University, Hangzhou 310018, China.
³ Department of Computer Science, University of Wisconsin, Milwaukee 53211, USA.

PMID: 25086274
DOI: 10.1016/j.jmgm.2014.06.012

Abstract

In order to compare the similarity between two protein models, a shape analysis algorithm based on skeleton extraction is presented in this paper. It firstly extracts the skeleton of a given protein surface by an improved Multi-resolution Reeb Graph (MRG) method. A number of points on the model surface are then collected to compute the local diameter (LD) according to the skeleton. Finally the LD frequency is calculated to build up the line chart, which is employed to analyze the shape similarity between protein models. Experimental results show that the similarity comparison using the proposed shape descriptor is more accurate especially for protein models with large deformations.

Keywords: Local diameter; Protein shapes; Shape descriptor; Similarity comparison; Skeleton.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Computer Simulation
Models, Molecular*
Protein Conformation
Proteins / chemistry*
Software

Substances

Proteins