title: A Novel Cylindrical Representation for Characterizing Intrinsic Properties of Protein Sequences.
abstract: The composition and sequence order of amino acid residues are the two most important characteristics to describe a protein sequence. Graphical representations facilitate visualization of biological sequences and produce biologically useful numerical descriptors. In this paper, we propose a novel cylindrical representation by placing the 20 amino acid residue types in a circle and sequence positions along the z axis. This representation allows visualization of the composition and sequence order of amino acids at the same time. Ten numerical descriptors and one weighted numerical descriptor have been developed to quantitatively describe intrinsic properties of protein sequences on the basis of the cylindrical model. Their applications to similarity/dissimilarity analysis of nine ND5 proteins indicated that these numerical descriptors are more effective than several classical numerical matrices. Thus, the cylindrical representation obtained here provides a new useful tool for visualizing and charactering protein sequences. An online server is available at http://biophy.dzu.edu.cn:8080/CNumD/input.jsp .
authors.affiliation: †Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.|‡State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.
authors.forename: Jia-Feng
authors.initials: JF
authors.lastname: Yu
authors.affiliation: †Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
authors.forename: Xiang-Hua
authors.initials: XH
authors.lastname: Dou
authors.affiliation: †Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
authors.forename: Hong-Bo
authors.initials: HB
authors.lastname: Wang
authors.affiliation: ‡State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Sun
authors.affiliation: §Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4000, Australia.
authors.forename: Hui-Ying
authors.initials: HY
authors.lastname: Zhao
authors.affiliation: †Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.|∥College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
authors.forename: Ji-Hua
authors.initials: JH
authors.lastname: Wang
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D009154:Mutation; D009245:NADH Dehydrogenase / Q000737:chemistry / Q000235:genetics; D011506:Proteins / Q000737:chemistry* / Q000235:genetics
chemical_list: D011506:Proteins; D009245:NADH Dehydrogenase