ModBase, a database of annotated comparative protein structure models, and associated resources

被引：226

作者：

Pieper, Ursula ^{[1
,2
]}

Webb, Benjamin M. ^{[1
,2
]}

Barkan, David T. ^{[1
,2
,3
]}

Schneidman-Duhovny, Dina ^{[1
,2
]}

Schlessinger, Avner ^{[1
,2
]}

Braberg, Hannes ^{[4
]}

Yang, Zheng ^{[5
]}

Meng, Elaine C. ^{[5
]}

Pettersen, Eric F. ^{[5
]}

Huang, Conrad C. ^{[5
]}

Datta, Ruchira S. ^{[6
,7
]}

Sampathkumar, Parthasarathy ^{[8
]}

Madhusudhan, Mallur S. ^{[9
]}

Sjoelander, Kimmen ^{[6
,7
]}

Ferrin, Thomas E. ^{[5
]}

Burley, Stephen K. ^{[8
]}

Sali, Andrej ^{[1
,2
]}

机构：

[1] Univ Calif San Francisco, Dept Pharmaceut Chem, Dept Bioengn & Therapeut Sci, San Francisco, CA 94158 USA

[2] Univ Calif San Francisco, Calif Inst Quantitat Biosci, San Francisco, CA 94158 USA

[3] Univ Calif San Francisco, Grad Grp Bioinformat, San Francisco, CA 94158 USA

[4] Univ Calif San Francisco, Grad Grp Biophys, San Francisco, CA 94158 USA

[5] Univ Calif San Francisco, Dept Pharmaceut Chem, San Francisco, CA 94143 USA

[6] Univ Calif Berkeley, Dept Bioengn, Inst QB3, Berkeley, CA 94720 USA

[7] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA

[8] Eli Lilly & Co, San Diego, CA 92121 USA

[9] Bioinformat Inst, Singapore 138671, Singapore

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

基金：

美国国家科学基金会; 美国国家卫生研究院;

关键词：

VARIABLE-GAP PENALTY; BIOTIN CARBOXYLASE; X-RAY; PREDICTION; SEQUENCE; SCATTERING; DISCOVERY; INFERENCE; ALIGNMENT; GENOMICS;

D O I：

10.1093/nar/gkq1091

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：

ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org/modeller/). ModBase currently contains 10 355 444 reliable models for domains in 2 421 920 unique protein sequences. ModBase allows users to update comparative models on demand, and request modeling of additional sequences through an interface to the ModWeb modeling server (http://salilab.org/modweb). ModBase models are available through the ModBase interface as well as the Protein Model Portal (http://www.proteinmodelportal.org/). Recently developed associated resources include the SALIGN server for multiple sequence and structure alignment (http://salilab.org/salign), the ModEval server for predicting the accuracy of protein structure models (http://salilab.org/modeval), the PCSS server for predicting which peptides bind to a given protein (http://salilab.org/pcss) and the FoXS server for calculating and fitting Small Angle X-ray Scattering profiles (http://salilab.org/foxs).

引用

页码：D465 / D474

页数：10

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