Three-dimensional protein model similarity analysis based on salient shape index

BMC Bioinformatics

Research Article

Zhong Li¹  Bo Yao¹  Meng Ding¹  Minhong Chen¹ 

[1] Departments of Mathematical Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China;

关键词: Protein model;    Shape index;    Salient geometric feature;    Shape analysis;   

DOI  :  10.1186/s12859-016-0983-z

 received in 2015-09-14, accepted in 2016-03-09,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundProteins play a special role in bioinformatics. The surface shape of a protein, which is an important characteristic of the protein, defines a geometric and biochemical domain where the protein interacts with other proteins. The similarity analysis among protein models has become an important topic of protein analysis, by which it can reveal the structure and the function of proteins.ResultsIn this paper, a new protein similarity analysis method based on three-dimensional protein models is proposed. It constructs a feature matrix descriptor for each protein model combined by calculating the shape index (SI) and the related salient geometric feature (SGF), and then analyzes the protein model similarity by using this feature matrix and the extended grey relation analysis.ConclusionsWe compare our method to the Multi-resolution Reeb Graph (MRG) skeleton method, the L1-medial skeleton method and the local-diameter descriptor method. Experimental results show that our protein similarity analysis method is accurate and reliable while keeping the high computational efficiency.

【 授权许可】

CC BY   
© Yao et al. 2016