title: Protein Sequence Comparison Based on Physicochemical Properties and the Position-Feature Energy Matrix.
abstract: We develop a novel position-feature-based model for protein sequences by employing physicochemical properties of 20 amino acids and the measure of graph energy. The method puts the emphasis on sequence order information and describes local dynamic distributions of sequences, from which one can get a characteristic B-vector. Afterwards, we apply the relative entropy to the sequences representing B-vectors to measure their similarity/dissimilarity. The numerical results obtained in this study show that the proposed methods leads to meaningful results compared with competitors such as Clustal W.
authors.affiliation: School of Mathematics and Statistics, Shandong University at Weihai, Weihai, 264209, China.
authors.forename: Lulu
authors.initials: L
authors.lastname: Yu
authors.affiliation: School of Mathematics and Statistics, Shandong University at Weihai, Weihai, 264209, China. zhangys@sdu.edu.cn.
authors.forename: Yusen
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Faculty of Science, University of Kragujevac, P. O. Box 60, Kragujevac, 34000, Serbia.
authors.forename: Ivan
authors.initials: I
authors.lastname: Gutman
authors.affiliation: Center for Combinatorics and LPMC, Nankai University, Tianjin, 300071, China.
authors.forename: Yongtang
authors.initials: Y
authors.lastname: Shi
authors.affiliation: Department of Mechatronics and Biomedical Computer Science, UMIT, Hall in Tyrol, Austria.|College of Computer and Control Engineering, Nankai University, Tianjin, 300071, China.
authors.forename: Matthias
authors.initials: M
authors.lastname: Dehmer
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D021301:Antifreeze Proteins / Q000737:chemistry; D055598:Chemical Phenomena; D019277:Entropy; D006801:Humans; D007526:Isoelectric Point; D009716:Numerical Analysis, Computer-Assisted; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D014168:Transferrin / Q000737:chemistry; D055544:beta-Globins / Q000737:chemistry
chemical_list: D021301:Antifreeze Proteins; D011506:Proteins; D014168:Transferrin; D055544:beta-Globins