Nucleic Acids Research Advance Access originally published online on November 4, 2008
Nucleic Acids Research 2009 37(Database issue):D333-D337; doi:10.1093/nar/gkn855
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Nucleic Acids Research, 2009, Vol. 37, Database issue D333-D337
© 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.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions
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.
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