Protein structure homology modeling using SWISS-MODEL workspace

被引：1001

作者：

Bordoli, Lorenza ^{[1
]}

Kiefer, Florian ^{[1
]}

Arnold, Konstantin ^{[1
]}

Benkert, Pascal ^{[1
]}

Battey, James ^{[1
]}

Schwede, Torsten ^{[1
]}

机构：

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

来源：

NATURE PROTOCOLS | 2009年 / 4卷 / 01期

关键词：

STRUCTURE PREDICTION; KINASE-C; DNA GLYCOSYLASES; MEAN FORCE; SEQUENCE; POTENTIALS; DATABASE; REGIONS; QUALITY; REPAIR;

D O I：

10.1038/nprot.2008.197

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Homology modeling aims to build three-dimensional protein structure models using experimentally determined structures of related family members as templates. SWISS-MODEL workspace is an integrated Web-based modeling expert system. For a given target protein, a library of experimental protein structures is searched to identify suitable templates. On the basis of a sequence alignment between the target protein and the template structure, a three-dimensional model for the target protein is generated. Model quality assessment tools are used to estimate the reliability of the resulting models. Homology modeling is currently the most accurate computational method to generate reliable structural models and is routinely used in many biological applications. Typically, the computational effort for a modeling project is less than 2 h. However, this does not include the time required for visualization and interpretation of the model, which may vary depending on personal experience working with protein structures.

引用

页码：1 / 13

页数：13

共 77 条

[1] Determining the architectures of macromolecular assemblies [J].

Alber, Frank ;

Dokudovskaya, Svetlana ;

Veenhoff, Liesbeth M. ;

Zhang, Wenzhu ;

Kipper, Julia ;

Devos, Damien ;

Suprapto, Adisetyantari ;

Karni-Schmidt, Orit ;

Williams, Rosemary ;

Chait, Brian T. ;

Rout, Michael P. ;

Sali, Andrej .

NATURE, 2007, 450 (7170) :683-694

[2] Protein complexes:: structure prediction challenges for the 21st century [J].

Aloy, P ;

Pichaud, M ;

Russell, RB .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 2005, 15 (01) :15-22

[3] A new protein superfamily includes two novel 3-methyladenine DNA glycosylases from Bacillus cereus, AlkC and AlkD [J].

Alseth, I ;

Rognes, T ;

Lindbäck, T ;

Solberg, I ;

Robertsen, K ;

Kristiansen, KI ;

Mainieri, D ;

Lillehagen, L ;

Kolsto, AB ;

Bjorås, M .

MOLECULAR MICROBIOLOGY, 2006, 59 (05) :1602-1609

[4] 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

[5] SCOP database in 2004: refinements integrate structure and sequence family data [J].

Andreeva, A ;

Howorth, D ;

Brenner, SE ;

Hubbard, TJP ;

Chothia, C ;

Murzin, AG .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D226-D229

[6]

[Anonymous], 1996, Biomolecular Simulation: the GROMOS96 Manual and User Guide

[7] The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling [J].

Arnold, K ;

Bordoli, L ;

Kopp, J ;

Schwede, T .

BIOINFORMATICS, 2006, 22 (02) :195-201

[8] Protein structure prediction and structural genomics [J].

Baker, D ;

Sali, A .

SCIENCE, 2001, 294 (5540) :93-96

[9]

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

[10]

Bates PA, 2001, PROTEINS, P39

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