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
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  T. Yoshida, K. Nagasaki, Y. Takashima, Y. Shirai, Y. Tomaru, Y. Takao, S. Sakamoto, S. Hiroishi, and H. Ogata Ma-LMM01 Infecting Toxic Microcystis aeruginosa Illuminates Diverse Cyanophage Genome Strategies J. Bacteriol., March 1, 2008; 190(5): 1762 - 1772. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Fukami-Kobayashi, Y. Minezaki, Y. Tateno, and K. Nishikawa A Tree of Life Based on Protein Domain Organizations Mol. Biol. Evol., May 1, 2007; 24(5): 1181 - 1189. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Homma, S. Fukuchi, Y. Nakamura, T. Gojobori, and K. Nishikawa Gene Cluster Analysis Method Identifies Horizontally Transferred Genes with High Reliability and Indicates that They Provide the Main Mechanism of Operon Gain in 8 Species of {gamma}-Proteobacteria Mol. Biol. Evol., March 1, 2007; 24(3): 805 - 813. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Kosuge, T. Abe, T. Okido, N. Tanaka, M. Hirahata, Y. Maruyama, J. Mashima, A. Tomiki, M. Kurokawa, R. Himeno, et al. Exploration and Grading of Possible Genes from 183 Bacterial Strains by a Common Protocol to Identification of New Genes: Gene Trek in Prokaryote Space (GTPS) DNA Res, January 1, 2006; 13(6): 245 - 254. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Itou, U. Okada, H. Suzuki, M. Yao, M. Wachi, N. Watanabe, and I. Tanaka The CGL2612 Protein from Corynebacterium glutamicum Is a Drug Resistance-related Transcriptional Repressor: STRUCTURAL AND FUNCTIONAL ANALYSIS OF A NEWLY IDENTIFIED TRANSCRIPTION FACTOR FROM GENOMIC DNA ANALYSIS J. Biol. Chem., November 18, 2005; 280(46): 38711 - 38719. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Minezaki, K. Homma, and K. Nishikawa Genome-Wide Survey of Transcription Factors in Prokaryotes Reveals Many Bacteria-Specific Families Not Found in Archaea DNA Res, January 1, 2005; 12(5): 269 - 280. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Zhang and J. Skolnick Tertiary Structure Predictions on a Comprehensive Benchmark of Medium to Large Size Proteins Biophys. J., October 1, 2004; 87(4): 2647 - 2655. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Arai, K. Okumura, M. Satake, and T. Shimizu Proteome-wide functional classification and identification of prokaryotic transmembrane proteins by transmembrane topology similarity comparison Protein Sci., August 1, 2004; 13(8): 2170 - 2183. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Zhang and J. Skolnick Automated structure prediction of weakly homologous proteins on a genomic scale PNAS, May 18, 2004; 101(20): 7594 - 7599. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Fleming, A. Muller, R. M. MacCallum, and M. J. E. Sternberg 3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes Nucleic Acids Res., January 1, 2004; 32(90001): D245 - 250. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. M. Singh and D. Murray Molecular modeling of the membrane targeting of phospholipase C pleckstrin homology domains Protein Sci., September 1, 2003; 12(9): 1934 - 1953. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Nakashima, S. Fukuchi, and K. Nishikawa Compositional Changes in RNA, DNA and Proteins for Bacterial Adaptation to Higher and Lower Temperatures J. Biochem., April 1, 2003; 133(4): 507 - 513. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Fukami-Kobayashi, Y. Tateno, and K. Nishikawa Parallel Evolution of Ligand Specificity Between LacI/GalR Family Repressors and Periplasmic Sugar-Binding Proteins Mol. Biol. Evol., February 1, 2003; 20(2): 267 - 277. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Yamaguchi, M. Iwadate, E.-i. Suzuki, K. Yura, S. Kawakita, H. Umeyama, and M. Go Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species Nucleic Acids Res., January 1, 2003; 31(1): 463 - 468. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Kihara, Y. Zhang, H. Lu, A. Kolinski, and J. Skolnick Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma genitalium genome PNAS, April 30, 2002; 99(9): 5993 - 5998. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Kihara, Y. Zhang, H. Lu, A. Kolinski, and J. Skolnick Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma genitalium genome PNAS, April 30, 2002; 99(9): 5993 - 5998. [Abstract] [Full Text] [PDF]
|
|