title: Predicting the types of J-proteins using clustered amino acids.
abstract: J-proteins are molecular chaperones and present in a wide variety of organisms from prokaryote to eukaryote. Based on their domain organizations, J-proteins can be classified into 4 types, that is, Type I, Type II, Type III, and Type IV. Different types of J-proteins play distinct roles in influencing cancer properties and cell death. Thus, reliably annotating the types of J-proteins is essential to better understand their molecular functions. In the present work, a support vector machine based method was developed to identify the types of J-proteins using the tripeptide composition of reduced amino acid alphabet. In the jackknife cross-validation, the maximum overall accuracy of 94% was achieved on a stringent benchmark dataset. We also analyzed the amino acid compositions by using analysis of variance and found the distinct distributions of amino acids in each family of the J-proteins. To enhance the value of the practical applications of the proposed model, an online web server was developed and can be freely accessed.
authors.affiliation: School of Public Health, Hebei United University, Tangshan 063000, China.
authors.forename: Pengmian
authors.initials: P
authors.lastname: Feng
authors.affiliation: Key Laboratory for Neuroinformation of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors.forename: Hao
authors.identifier: 0000-0001-6265-2862
authors.initials: H
authors.lastname: Lin
authors.affiliation: Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China.
authors.forename: Wei
authors.identifier: 0000-0002-6857-7696
authors.initials: W
authors.lastname: Chen
authors.affiliation: The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot 010021, China.
authors.forename: Yongchun
authors.initials: Y
authors.lastname: Zuo
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics*; D000596:Amino Acids / Q000235:genetics*; D001185:Artificial Intelligence; D030562:Databases, Protein; D050956:HSP40 Heat-Shock Proteins / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D018832:Molecular Chaperones / Q000235:genetics*; D060388:Support Vector Machine
chemical_list: D000596:Amino Acids; D050956:HSP40 Heat-Shock Proteins; D018832:Molecular Chaperones