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  1. GTOP - Genomes To Protein structures
    Resource Category : Databases -> Structure Databases -> Protein structure

    Brief Description : Although large-scale genome projects generate an unprecedented number of protein sequences, most of them are experimentally uncharacterized. Prediction of the 3D structures of the proteins encoded by sequences provides important clues to their functions. We constructed the Genomes TO Protein structures and functions (GTOP) database, containing protein fold predictions of a huge number of sequences. Predictions by homology are mainly carried out with the PSI-BLAST program. GTOP also includes the results of other analyses, e.g. homology and motif search, detection of transmembrane helices and repetitive sequences. GTOP uses a graphical viewer to present the analytical results of each ORF in one page in a ecolor-barf format. The assigned 3D structures are presented by Chime plug-in or RasMol. The binding sites of ligands are also included, providing functional information. The GTOP server is available at http://spock.genes.nig.ac.jp/~genome/gtop.html.

    Institute/s :
    Center for Information Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
    Address of Institute/s :
    Center for Information Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
    Country : Japan

    Associated Institutes :

    • Center for Information Biology and DNA Data Bank of Japan
    • National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540
    • HOLONICS Corporation, Soeji 85, Numazu, Shizuoka 411-0803
    • Department of Bioinformatics, Maebashi Institute of Technology, Kamisadori 460-1, Maebashi, Gunma 371-0816, Japan

    Associated Country : Japan


    Authors/Contributors : Satoshi Fukuchi; Keiichi Homma; Shigetaka Sakamoto; Hideaki Sugawara; Yoshio Tateno; Takashi Gojobori; Ken Nishikawa
    Contact Email : sfukuchi@genes.nig.ac.jp
    Year : 2008
    Language : English