Nucleic Acids Research, 2002, Vol. 30, No. 1 294-298
© 2002 Oxford University Press
GTOP: a database of protein structures predicted from genome sequences
1Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, 1-111 Yata, Mishima, Shizuoka 411-8540, Japan, 2Japan Science and Technology Corporation, 1–8 Honcho, 4-chome, Kawaguchi City, Saitama, 332-0012, Japan and 3Mitsubishi Research Institute, Inc., 3–6 Otemachi, 2-chome, Chiyoda-ku, Tokyo 100-8141, Japan
Large-scale genome projects generate an unprecedented number of protein sequences, most of them are experimentally uncharacterized. Predicting the 3D structures of sequences provides important clues as 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 are mainly carried out with the homology search program PSI-BLAST, currently the most popular among high-sensitivity profile search methods. GTOP also includes the results of other analyses, e.g. homology and motif search, detection of transmembrane helices and repetitive sequences. We have completed analyzing the sequences of 41 organisms, with the number of proteins exceeding 120 000 in total. GTOP uses a graphical viewer to present the analytical results of each ORF in one page in a ‘color-bar’ 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.
* To whom correspondence should be addresssed. Tel: +81 559 81 6859; Fax: +81 559 81 6889; Email: knishika{at}genes.nig.ac.jp
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