GTOP

http://spock.genes.nig.ac.jp/~genome/gtop.html

Fukuchi, S., Homma, K., Sakamoto, S., Nishikawa, K.

Center for Information Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan

Database 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 ‘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.

Recent Developments

As of September 2002, 41 newly sequenced genomes have been analyzed and the results have been incorporated to GTOP, making it a comprehensive database containing 82 genomes and 276,389 ORFs in total. In addition information on exon/intron structures has been included in analyses of the eukaryotic genomes and viewers have been developed to indicate exon boundaries by colors both in primary and 3D structures. Furthermore the GO (Gene ontology) terms assigned to each gene according to links with Swiss-prot keywords and Pfam domains have been added to the display. Lastly ftp utility has been made available so that results of GTOP analyses can be downloaded.

REFERENCES

"GTOP: a database of protein structures predicted from genome sequence." Kawabata T, Fukuchi S, Homma K, Ota M, Araki J, Ito T, Ichiyoshi N, Nishikawa K. Nucleic Acids Res 2002 Jan 1;30(1):294-8