IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature

被引：76

作者：

Fukuchi, Satoshi ^{[1
]}

Sakamoto, Shigetaka ^{[2
]}

Nobe, Yukiko ^{[3
]}

Murakami, Seiko D. ^{[3
]}

Amemiya, Takayuki ^{[3
]}

Hosoda, Kazuo ^{[1
]}

Koike, Ryotaro ^{[3
]}

Hiroaki, Hidekazu ^{[4
]}

Ota, Motonori ^{[3
]}

机构：

[1] Maebashi Inst Technol, Fac Engn, Maebashi, Gunma 3710816, Japan

[2] HOLONICS Corp, Shizuoka 4110803, Japan

[3] Nagoya Univ, Grad Sch Informat Sci, Nagoya, Aichi 4648601, Japan

[4] Nagoya Univ, Grad Sch Sci, Nagoya, Aichi 4648601, Japan

来源：

NUCLEIC ACIDS RESEARCH | 2012年 / 40卷 / D1期

关键词：

UNSTRUCTURED PROTEINS; DOMAIN; DATABASE; P53; CLASSIFICATION;

D O I：

10.1093/nar/gkr884

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：

IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collection of knowledge on experimentally verified intrinsically disordered proteins. IDEAL contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. In particular, IDEAL explicitly describes protean segments that can be transformed from a disordered state to an ordered state. Since in most cases they can act as molecular recognition elements upon binding of partner proteins, IDEAL provides a data resource for functional regions of intrinsically disordered proteins. The information in IDEAL is provided on a user-friendly graphical view and in a computer-friendly XML format.

引用

页码：D507 / D511

页数：5

共 25 条

[1] 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

[2] The Universal Protein Resource (UniProt) in 2010 [J].

Apweiler, Rolf ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Alam-Faruque, Yasmin ;

Antunes, Ricardo ;

Barrell, Daniel ;

Bely, Benoit ;

Bingley, Mark ;

Binns, David ;

Bower, Lawrence ;

Browne, Paul ;

Chan, Wei Mun ;

Dimmer, Emily ;

Eberhardt, Ruth ;

Fedotov, Alexander ;

Foulger, Rebecca ;

Garavelli, John ;

Huntley, Rachael ;

Jacobsen, Julius ;

Kleen, Michael ;

Laiho, Kati ;

Leinonen, Rasko ;

Legge, Duncan ;

Lin, Quan ;

Liu, Wudong ;

Luo, Jie ;

Orchard, Sandra ;

Patient, Samuel ;

Poggioli, Diego ;

Pruess, Manuela ;

Corbett, Matt ;

di Martino, Giuseppe ;

Donnelly, Mike ;

van Rensburg, Pieter ;

Bairoch, Amos ;

Bougueleret, Lydie ;

Xenarios, Ioannis ;

Altairac, Severine ;

Auchincloss, Andrea ;

Argoud-Puy, Ghislaine ;

Axelsen, Kristian ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte ;

Bolleman, Jerven ;

Bollondi, Laurent ;

Boutet, Emmanuel ;

Quintaje, Silvia Braconi ;

Breuza, Lionel .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D142-D148

[3]

Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkh121, 10.1093/nar/gkr1065]

[4] p53 contains large unstructured regions in its native state [J].

Bell, S ;

Klein, C ;

Müller, L ;

Hansen, S ;

Buchner, J .

JOURNAL OF MOLECULAR BIOLOGY, 2002, 322 (05) :917-927

[5] The N-terminal domain of p53 is natively unfolded [J].

Dawson, R ;

Müller, L ;

Dehner, A ;

Klein, C ;

Kessler, H ;

Buchner, J .

JOURNAL OF MOLECULAR BIOLOGY, 2003, 332 (05) :1131-1141

[6] Intrinsically unstructured proteins and their functions [J].

Dyson, HJ ;

Wright, PE .

NATURE REVIEWS MOLECULAR CELL BIOLOGY, 2005, 6 (03) :197-208

[7] Binary classification of protein molecules into intrinsically disordered and ordered segments [J].

Fukuchi, Satoshi ;

Hosoda, Kazuo ;

Homma, Keiichi ;

Gojobori, Takashi ;

Nishikawa, Ken .

BMC STRUCTURAL BIOLOGY, 2011, 11

[8] Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure [J].

Gough, J ;

Karplus, K ;

Hughey, R ;

Chothia, C .

JOURNAL OF MOLECULAR BIOLOGY, 2001, 313 (04) :903-919

[9] ELM: the status of the 2010 eukaryotic linear motif resource [J].

Gould, Cathryn M. ;

Diella, Francesca ;

Via, Allegra ;

Puntervoll, Pal ;

Gemuend, Christine ;

Chabanis-Davidson, Sophie ;

Michael, Sushama ;

Sayadi, Ahmed ;

Bryne, Jan Christian ;

Chica, Claudia ;

Seiler, Markus ;

Davey, Norman E. ;

Haslam, Niall ;

Weatheritt, Robert J. ;

Budd, Aidan ;

Hughes, Tim ;

Pas, Jakub ;

Rychlewski, Leszek ;

Trave, Gilles ;

Aasland, Rein ;

Helmer-Citterich, Manuela ;

Linding, Rune ;

Gibson, Toby J. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D167-D180

[10] The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution [J].

Greene, Lesley H. ;

Lewis, Tony E. ;

Addou, Sarah ;

Cuff, Alison ;

Dallman, Tim ;

Dibley, Mark ;

Redfern, Oliver ;

Pearl, Frances ;

Nambudiry, Rekha ;

Reid, Adam ;

Sillitoe, Ian ;

Yeats, Corin ;

Thornton, Janet M. ;

Orengo, Christine A. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D291-D297

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