Skip Navigation



Nucleic Acids Research Advance Access published online on November 4, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn855
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1704K) Freely available
Right arrow Screen PDF (389K) Freely available
Right arrowOA All Versions of this Article:
37/suppl_1/D333    most recent
gkn855v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Fukuchi, S.
Right arrow Articles by Nishikawa, K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Fukuchi, S.
Right arrow Articles by Nishikawa, K.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions

Satoshi Fukuchi1,*, Keiichi Homma1, Shigetaka Sakamoto2, Hideaki Sugawara1, Yoshio Tateno1, Takashi Gojobori1 and Ken Nishikawa3

1Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, 2HOLONICS Corporation, Soeji 85, Numazu, Shizuoka 411-0803 and 3Department of Bioinformatics, Maebashi Institute of Technology, Kamisadori 460-1, Maebashi, Gunma 371-0816, Japan

*To whom correspondence should be addressed. Tel: +81 55 981 6837; Fax: +81 55 981 6889; Email: sfukuchi{at}genes.nig.ac.jp

Received September 12, 2008. Revised October 15, 2008. Accepted October 16, 2008.

The Genomes TO Protein Structures and Functions (GTOP) database (http://spock.genes.nig.ac.jp/~genome/gtop.html) freely provides an extensive collection of information on protein structures and functions obtained by application of various computational tools to the amino acid sequences of entirely sequenced genomes. GTOP contains annotations of 3D structures, protein families, functions, and other useful data of a protein of interest in user-friendly ways to give a deep insight into the protein structure. From the initial 1999 version, GTOP has been continually updated to reap the fruits of genome projects and augmented to supply novel information, in particular intrinsically disordered regions. As intrinsically disordered regions constitute a considerable fraction of proteins and often play crucial roles especially in eukaryotes, their assignments give important additional clues to the functionality of proteins. Additionally, we have incorporated the following features into GTOP: a platform independent structural viewer, results of HMM searches against SCOP and Pfam, secondary structure predictions, color display of exon boundaries in eukaryotic proteins, assignments of gene ontology terms, search tools, and master files.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
Y. Yamazaki, R. Akashi, Y. Banno, T. Endo, H. Ezura, K. Fukami-Kobayashi, K. Inaba, T. Isa, K. Kamei, F. Kasai, et al.
NBRP databases: databases of biological resources in Japan
Nucleic Acids Res., November 24, 2009; (2009) gkp996v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Yamasaki, K. Murakami, J.-i. Takeda, Y. Sato, A. Noda, R. Sakate, T. Habara, H. Nakaoka, F. Todokoro, A. Matsuya, et al.
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts
Nucleic Acids Res., November 23, 2009; (2009) gkp1020v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Kwon, Y. Shigemoto, Y. Kuwana, and H. Sugawara
Web API for biology with a workflow navigation system
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W11 - W16.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.