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

被引：22

作者：

Fukuchi, Satoshi ^{[1
,2
]}

Homma, Keiichi ^{[1
,2
]}

Sakamoto, Shigetaka ^{[3
]}

Sugawara, Hideaki ^{[1
,2
]}

Tateno, Yoshio ^{[1
,2
]}

Gojobori, Takashi ^{[1
,2
]}

Nishikawa, Ken ^{[4
]}

机构：

[1] Natl Inst Genet, Ctr Informat Biol, Mishima, Shizuoka 4118540, Japan

[2] Natl Inst Genet, DNA Data Bank Japan, Mishima, Shizuoka 4118540, Japan

[3] HOLONICS Corp, Shizuoka 4110803, Japan

[4] Maebashi Inst Technol, Dept Bioinformat, Gunma 3710816, Japan

来源：

NUCLEIC ACIDS RESEARCH | 2009年 / 37卷

基金：

日本科学技术振兴机构;

关键词：

INTRINSICALLY DISORDERED REGIONS; FAMILIES;

D O I：

10.1093/nar/gkn855

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Genomes TO Protein Structures and Functions (GTOP) database (http://spock.genes.nig.ac.jp/similar to 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.

引用

页码：D333 / D337

页数：5

共 22 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2] Data growth and its impact on the SCOP database: new developments [J].

Andreeva, Antonina ;

Howorth, Dave ;

Chandonia, John-Marc ;

Brenner, Steven E. ;

Hubbard, Tim J. P. ;

Chothia, Cyrus ;

Murzin, Alexey G. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D419-D425

[3] The Universal Protein Resource (UniProt) [J].

Bairoch, Amos ;

Bougueleret, Lydie ;

Altairac, Severine ;

Amendolia, Valeria ;

Auchincloss, Andrea ;

Puy, Ghislaine Argoud ;

Axelsen, Kristian ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte ;

Bollondi, Laurent ;

Boutet, Emmanuel ;

Quintaje, Silvia Braconi ;

Breuza, Lionel ;

Bridge, Alan ;

Saux, Virginie Bulliard-Le ;

decastro, Edouard ;

Ciampina, Luciane ;

Coral, Danielle ;

Coudert, Elisabeth ;

Cusin, Isabelle ;

David, Fabrice ;

Delbard, Gwennaelle ;

Dornevil, Dolnide ;

Duek-Roggli, Paula ;

Duvaud, Severine ;

Estreicher, Anne ;

Famiglietti, Livia ;

Farriol-Mathis, Nathalie ;

Ferro, Serenella ;

Feuermann, Marc ;

Gasteiger, Elisabeth ;

Gateau, Alain ;

Gehant, Sebastian ;

Gerritsen, Vivienne ;

Gos, Arnaud ;

Gruaz-Gumowski, Nadine ;

Hinz, Ursula ;

Hulo, Chantal ;

Hulo, Nicolas ;

Innocenti, Alessandro ;

James, Janet ;

Jain, Eric ;

Jimenez, Silvia ;

Jungo, Florence ;

Junker, Vivien ;

Keller, Guillaume ;

Lachaize, Corinne ;

Lane-Guermonprez, Lydie ;

Langendijk-Genevaux, Petra .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D190-D195

[4] Intrinsically disordered protein [J].

Dunker, AK ;

Lawson, JD ;

Brown, CJ ;

Williams, RM ;

Romero, P ;

Oh, JS ;

Oldfield, CJ ;

Campen, AM ;

Ratliff, CR ;

Hipps, KW ;

Ausio, J ;

Nissen, MS ;

Reeves, R ;

Kang, CH ;

Kissinger, CR ;

Bailey, RW ;

Griswold, MD ;

Chiu, M ;

Garner, EC ;

Obradovic, Z .

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 2001, 19 (01) :26-59

[5] The Pfam protein families database [J].

Finn, Robert D. ;

Tate, John ;

Mistry, Jaina ;

Coggill, Penny C. ;

Sammut, Stephen John ;

Hotz, Hans-Rudolf ;

Ceric, Goran ;

Forslund, Kristoffer ;

Eddy, Sean R. ;

Sonnhammer, Erik L. L. ;

Bateman, Alex .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D281-D288

[6] Remediation of the protein data bank archive [J].

Henrick, Kim ;

Feng, Zukang ;

Bluhm, Wolfgang F. ;

Dimitropoulos, Dimitris ;

Doreleijers, Jurgen F. ;

Dutta, Shuchismita ;

Flippen-Anderson, Judith L. ;

Ionides, John ;

Kamada, Chisa ;

Krissinel, Eugene ;

Lawson, Catherine L. ;

Markley, John L. ;

Nakamura, Haruki ;

Newman, Richard ;

Shimizu, Yukiko ;

Swaminathan, Jawahar ;

Velankar, Sameer ;

Ory, Jeramia ;

Ulrich, Eldon L. ;

Vranken, Wim ;

Westbrook, John ;

Yamashita, Reiko ;

Yang, Huanwang ;

Young, Jasmine ;

Yousufuddin, Muhammed ;

Berman, Helen M. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D426-D433

[7] Alternative splice variants encoding unstable protein domains exist in the human brain [J].

Homma, K ;

Kikuno, RF ;

Nagase, T ;

Ohara, O ;

Nishikawa, K .

JOURNAL OF MOLECULAR BIOLOGY, 2004, 343 (05) :1207-1220

[8]

HULO N, 2008, NUCLEIC ACIDS RES, V245, P20

[9] GTOP: a database of protein structures predicted from genome sequences [J].

Kawabata, T ;

Fukuchi, S ;

Homma, K ;

Ota, M ;

Araki, J ;

Ito, T ;

Ichiyoshi, N ;

Nishikawa, K .

NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :294-298

[10] Induced α-helix structure in AF1 of the androgen receptor upon binding transcription factor TFIIF [J].

Kumar, R ;

Betney, R ;

Li, JQ ;

Thompson, EB ;

McEwan, IJ .

BIOCHEMISTRY, 2004, 43 (11) :3008-3013

← 1 2 3 →