title: Mathematical characterization of protein transmembrane regions.
abstract: Graphical bioinformatics has paved a unique way of mathematical characterization of proteins and proteomic maps. The graphics representations and the corresponding mathematical descriptors have proved to be useful and have provided unique solutions to problems related to identification, comparisons, and analyses of protein sequences and proteomics maps. Based on sequence information alone, these descriptors are independent from physiochemical properties of amino acids and evolutionary information. In this work, we have presented invariants from amino acid adjacency matrix and decagonal isometries matrix as potential descriptors of protein sequences. Encoding protein sequences into amino acid adjacency matrix is already well established. We have shown its application in classification of transmembrane and nontransmembrane regions of membrane protein sequences. We have introduced the dodecagonal isometries matrix, which is a novel method of encoding protein sequences based on decagonal isometries group.
authors.affiliation: Laboratory of Chemometrics, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia.
authors.forename: Amrita
authors.initials: A
authors.lastname: Roy Choudhury
authors.forename: Nikolay
authors.initials: N
authors.lastname: Zhukov
authors.forename: Marjana
authors.initials: M
authors.lastname: Novič
mesh_terms: D000595:Amino Acid Sequence; D002462:Cell Membrane / Q000737:chemistry*; D003198:Computer Simulation; D008565:Membrane Proteins / Q000737:chemistry*; D008956:Models, Chemical; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D008565:Membrane Proteins