title: Three-dimensional protein model similarity analysis based on salient shape index.
abstract: BACKGROUND
  Proteins 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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  We 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.
authors.affiliation: Departments of Mathematical Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Yao
authors.affiliation: Departments of Mathematical Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China. lizhong@zstu.edu.cn.
authors.forename: Zhong
authors.initials: Z
authors.lastname: Li
authors.affiliation: Departments of Mathematical Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
authors.forename: Meng
authors.initials: M
authors.lastname: Ding
authors.affiliation: Departments of Mathematical Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
authors.forename: Minhong
authors.initials: M
authors.lastname: Chen
mesh_terms: D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins
keywords: Protein model; Salient geometric feature; Shape analysis; Shape index