TY - JOUR
T1 - The GTOP database in 2009
T2 - Updated content and novel features to expand and deepen insights into protein structures and functions
AU - Fukuchi, Satoshi
AU - Homma, Keiichi
AU - Sakamoto, Shigetaka
AU - Sugawara, Hideaki
AU - Tateno, Yoshio
AU - Gojobori., Takashi
AU - Nishikawa, Ken
N1 - Funding Information:
The GTOP database is supported in part by the Target Protein Research Program from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and in part by the Bioinformatics Research and Development Project from the Japan Science and Technology Agency. Funding for open access publication charge: the Ministry of Education, Culture, Sports, Science and Technology of Japan.
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=58149250634&partnerID=8YFLogxK
U2 - 10.1093/nar/gkn855
DO - 10.1093/nar/gkn855
M3 - Article
C2 - 18987007
AN - SCOPUS:58149250634
SN - 0305-1048
VL - 37
SP - D333-D337
JO - NUCLEIC ACIDS RESEARCH
JF - NUCLEIC ACIDS RESEARCH
IS - SUPPL. 1
ER -