title: The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions.
abstract: 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.
authors.affiliation: Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan. sfukuchi@genes.nig.ac.jp
authors.forename: Satoshi
authors.initials: S
authors.lastname: Fukuchi
authors.forename: Keiichi
authors.initials: K
authors.lastname: Homma
authors.forename: Shigetaka
authors.initials: S
authors.lastname: Sakamoto
authors.forename: Hideaki
authors.initials: H
authors.lastname: Sugawara
authors.forename: Yoshio
authors.initials: Y
authors.lastname: Tateno
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
authors.forename: Ken
authors.initials: K
authors.lastname: Nishikawa
mesh_terms: D030562:Databases, Protein; D005091:Exons; D023281:Genomics; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000235:genetics* / Q000502:physiology; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D011506:Proteins