SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

被引：3761

作者：

Biasini, Marco ^{[1
,2
]}

Bienert, Stefan ^{[1
,2
]}

Waterhouse, Andrew ^{[1
,2
]}

Arnold, Konstantin ^{[1
,2
]}

Studer, Gabriel ^{[1
,2
]}

Schmidt, Tobias ^{[1
,2
]}

Kiefer, Florian ^{[1
,2
]}

Cassarino, Tiziano Gallo ^{[1
,2
]}

Bertoni, Martino ^{[1
,2
]}

Bordoli, Lorenza ^{[1
,2
]}

Schwede, Torsten ^{[1
,2
]}

机构：

[1] Univ Basel, Biozentrum, CH-4056 Basel, Switzerland

[2] SIB Swiss Inst Bioinformat, CH-4056 Basel, Switzerland

来源：

NUCLEIC ACIDS RESEARCH | 2014年 / 42卷 / W1期

关键词：

STRUCTURE PREDICTION; SECONDARY STRUCTURE; QUALITY; WEB; RECOGNITION; ENVIRONMENT; PDBVIEWER; SINGLE; SERVER; SCORE;

D O I：

10.1093/nar/gku340

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：

Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable models without the need for complex software packages or downloading large databases. Here, we describe the latest version of the SWISS-MODEL expert system for protein structure modelling. The SWISS-MODEL template library provides annotation of quaternary structure and essential ligands and co-factors to allow for building of complete structural models, including their oligomeric structure. The improved SWISS-MODEL pipeline makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the expected accuracy of the resulting models. The accuracy of the models generated by SWISS-MODEL is continuously evaluated by the CAMEO system. The new web site allows users to interactively search for templates, cluster them by sequence similarity, structurally compare alternative templates and select the ones to be used for model building. In cases where multiple alternative template structures are available for a protein of interest, a user-guided template selection step allows building models in different functional states.

引用

页码：W252 / W258

页数：7

共 35 条

[21] Assessment of the assessment: Evaluation of the model quality estimates in CASP10 [J].

Kryshtafovych, Andriy ;

Barbato, Alessandro ;

Fidelis, Krzysztof ;

Monastyrskyy, Bohdan ;

Schwede, Torsten ;

Tramontano, Anna .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2014, 82 :112-126

[22] lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests [J].

Mariani, Valerio ;

Biasini, Marco ;

Barbato, Alessandro ;

Schwede, Torsten .

BIOINFORMATICS, 2013, 29 (21) :2722-2728

[23] Assessment of template based protein structure predictions in CASP9 [J].

Mariani, Valerio ;

Kiefer, Florian ;

Schmidt, Tobias ;

Haas, Juergen ;

Schwede, Torsten .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2011, 79 :37-58

[24] CAD-score: A new contact area difference-based function for evaluation of protein structural models [J].

Olechnovic, Kliment ;

Kulberkyte, Eleonora ;

Venclovas, Ceslovas .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2013, 81 (01) :149-162

[25]

Poupon A, 2010, METHODS MOL BIOL, V609, P349, DOI 10.1007/978-1-60327-241-4_20

[26]

Remmert M, 2012, NAT METHODS, V9, P173, DOI [10.1038/NMETH.1818, 10.1038/nmeth.1818]

[27]

Rykunov Dmitry, 2009, Journal of Structural and Functional Genomics, V10, P95, DOI 10.1007/s10969-008-9044-9

[28] Benchmarking template selection and model quality assessment for high-resolution comparative modelling [J].

Sadowski, M. I. ;

Jones, D. T. .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2007, 69 (03) :476-485

[29] COMPARATIVE PROTEIN MODELING BY SATISFACTION OF SPATIAL RESTRAINTS [J].

SALI, A ;

BLUNDELL, TL .

JOURNAL OF MOLECULAR BIOLOGY, 1993, 234 (03) :779-815

[30]

Schmidt T., 2013, Drug discovery today

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