title: Evaluating protein similarity from coarse structures.
abstract: To unscramble the relationship between protein function and protein structure, it is essential to assess the protein similarity from different aspects. Although many methods have been proposed for protein structure alignment or comparison, alternative similarity measures are still strongly demanded due to the requirement of fast screening and query in large-scale structure databases. In this paper, we first formulate a novel representation of a protein structure, i.e., Feature Sequence of Surface (FSS). Then, a new score scheme is developed to measure the similarity between two representations. To verify the proposed method, numerical experiments are conducted in four different protein data sets. We also classify SARS coronavirus to verify the effectiveness of the new method. Furthermore, preliminary results of fast classification of the whole CATH v2.5.1 database based on the new macrostructure similarity are given as a pilot study. We demonstrate that the proposed approach to measure the similarities between protein structures is simple to implement, computationally efficient, and surprisingly fast. In addition, the method itself provides a new and quantitative tool to view a protein structure.
authors.affiliation: Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, No. 55 Zhongguancun East Road, Beijing, 100080, China. ywang@amss.ac.cn
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
authors.forename: Ling-Yun
authors.initials: LY
authors.lastname: Wu
authors.forename: Ji-Hong
authors.initials: JH
authors.lastname: Zhang
authors.forename: Zhong-Wei
authors.initials: ZW
authors.lastname: Zhan
authors.forename: Xiang-Sun
authors.initials: XS
authors.lastname: Zhang
authors.forename: Luonan
authors.initials: L
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D006801:Humans; D008958:Models, Molecular; D010363:Pattern Recognition, Automated / Q000379:methods; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D045473:Severe acute respiratory syndrome-related coronavirus / Q000378:metabolism; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software
chemical_list: D011506:Proteins