title: Novel numerical characterization of protein sequences based on individual amino acid and its application.
abstract: The hydrophobicity and hydrophilicity of amino acids play a very important role in protein folding and its interaction with the environment and other molecules, as well as its catalytic mechanism. Based on the two physicochemical indexes, a 2D graphical representation of protein sequences is introduced; meanwhile, a new numerical characteristic has been proposed to compute the distance of different sequences for analysis of sequence similarity/dissimilarity on the basis of this graphical representation. Furthermore, we apply the new distance in the similarities/dissimilarities of ND5 proteins of nine species and predict the four major classes based on the dataset containing 639 domains. The results show that the method is simple and effective.
authors.affiliation: Department of Mathematics, School of Science, Hebei University of Engineering, Handan 056038, China.
authors.forename: Yan-ping
authors.initials: YP
authors.lastname: Zhang
authors.affiliation: Graduate School at ShenZhen, Tsinghua University, Guangdong 518055, China.
authors.forename: Ya-jun
authors.initials: YJ
authors.lastname: Sheng
authors.affiliation: College of Mathematical Sciences and LPMC, Nankai University, Tianjin 300071, China.
authors.forename: Wei
authors.identifier: 0000-0002-2984-9003
authors.initials: W
authors.lastname: Zheng
authors.affiliation: Department of Mathematics, College of Science, Zhejiang Sci-Tech University, Hangzhou 310018, China.
authors.forename: Ping-an
authors.initials: PA
authors.lastname: He
authors.affiliation: College of Mathematical Sciences and LPMC, Nankai University, Tianjin 300071, China.
authors.forename: Ji-shuo
authors.initials: JS
authors.lastname: Ruan
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics*; D000596:Amino Acids / Q000737:chemistry / Q000235:genetics*; D019295:Computational Biology; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D020539:Sequence Analysis, Protein
chemical_list: D000596:Amino Acids; D011506:Proteins