title: Protein-protein interface prediction based on hexagon structure similarity.
abstract: Studies on protein-protein interaction are important in proteome research. How to build more effective models based on sequence information, structure information and physicochemical characteristics, is the key technology in protein-protein interface prediction. In this paper, we study the protein-protein interface prediction problem. We propose a novel method for identifying residues on interfaces from an input protein with both sequence and 3D structure information, based on hexagon structure similarity. Experiments show that our method achieves better results than some state-of-the-art methods for identifying protein-protein interface. Comparing to existing methods, our approach improves F-measure value by at least 0.03. On a common dataset consisting of 41 complexes, our method has overall precision and recall values of 63% and 57%. On Benchmark v4.0, our method has overall precision and recall values of 55% and 56%. On CAPRI targets, our method has overall precision and recall values of 52% and 55%.
authors.affiliation: School of Computer Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, PR China.
authors.forename: Fei
authors.initials: F
authors.lastname: Guo
authors.affiliation: School of Computer Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, PR China.
authors.forename: Yijie
authors.initials: Y
authors.lastname: Ding
authors.affiliation: Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong.
authors.forename: Shuai Cheng
authors.initials: SC
authors.lastname: Li
authors.affiliation: Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong.
authors.forename: Chao
authors.initials: C
authors.lastname: Shen
authors.affiliation: Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong; City University of Hong Kong Shenzhen Research Institute, Shenzhen Hi-Tech Industrial Park, Nanshan District, Shenzhen, PR China. Electronic address: cswangl@cityu.edu.hk.
authors.forename: Lusheng
authors.initials: L
authors.lastname: Wang
mesh_terms: D018360:Crystallography, X-Ray; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins
keywords: Hexagon structure; Neighborhood information; Protein–protein interface