Nucleic Acids Research, 2003, Vol. 31, No. 13 3381-3385
© 2003 Oxford University Press
SWISS-MODEL: an automated protein homology-modeling server
1 Biozentrum der Universität Basel, Klingelbergstr. 50-70, CH 4056 Basel, Switzerland 2 Swiss Institute of Bioinformatics, Basel, Switzerland 3 GlaxoSmithKline, Research Triangle Park, NC 27709, USA 4 Novartis AG, 4002 Basel, Switzerland
*To whom correspondence should be addressed. Tel: +41 612671581; Fax: +41 612671584; Email: torsten.schwede{at}unibas.ch
SWISS-MODEL (http://swissmodel.expasy.org) is a server for automated comparative modeling of three-dimensional (3D) protein structures. It pioneered the field of automated modeling starting in 1993 and is the most widely-used free web-based automated modeling facility today. In 2002 the server computed 120 000 user requests for 3D protein models. SWISS-MODEL provides several levels of user interaction through its World Wide Web interface: in the ‘first approach mode’ only an amino acid sequence of a protein is submitted to build a 3D model. Template selection, alignment and model building are done completely automated by the server. In the ‘alignment mode’, the modeling process is based on a user-defined target-template alignment. Complex modeling tasks can be handled with the ‘project mode’ using DeepView (Swiss-PdbViewer), an integrated sequence-to-structure workbench. All models are sent back via email with a detailed modeling report. WhatCheck analyses and ANOLEA evaluations are provided optionally. The reliability of SWISS-MODEL is continuously evaluated in the EVA-CM project. The SWISS-MODEL server is under constant development to improve the successful implementation of expert knowledge into an easy-to-use server.
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T. Nuutinen, H. Tossavainen, K. Fredriksson, P. Pirila, P. Permi, H. Pospiech, and J. E. Syvaoja The solution structure of the amino-terminal domain of human DNA polymerase {varepsilon} subunit B is homologous to C-domains of AAA+ proteins Nucleic Acids Res., September 1, 2008; 36(15): 5102 - 5110. [Abstract] [Full Text] [PDF]
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Y.-Y. Yao, K. L. Shrestha, Y.-J. Wu, H.-J. Tasi, C.-C. Chen, J.-M. Yang, A. Ando, C.-Y. Cheng, and Y.-K. Li Structural simulation and protein engineering to convert an endo-chitosanase to an exo-chitosanase Protein Eng. Des. Sel., September 1, 2008; 21(9): 561 - 566. [Abstract] [Full Text] [PDF]
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C. C. Hernandez, O. Zaika, and M. S. Shapiro A Carboxy-terminal Inter-Helix Linker As the Site of Phosphatidylinositol 4,5-Bisphosphate Action on Kv7 (M-type) K+ Channels J. Gen. Physiol., August 25, 2008; 132(3): 361 - 381. [Abstract] [Full Text] [PDF]
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I. Keren, L. Klipcan, A. Bezawork-Geleta, M. Kolton, F. Shaya, and O. Ostersetzer-Biran Characterization of the Molecular Basis of Group II Intron RNA Recognition by CRS1-CRM Domains J. Biol. Chem., August 22, 2008; 283(34): 23333 - 23342. [Abstract] [Full Text] [PDF]
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C. L. Carswell, M. D. Rigden, and J. E. Baenziger Expression, Purification, and Structural Characterization of CfrA, a Putative Iron Transporter from Campylobacter jejuni J. Bacteriol., August 15, 2008; 190(16): 5650 - 5662. [Abstract] [Full Text] [PDF]
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C. C. Heikaus, J. R. Stout, M. R. Sekharan, C. M. Eakin, P. Rajagopal, P. S. Brzovic, J. A. Beavo, and R. E. Klevit Solution Structure of the cGMP Binding GAF Domain from Phosphodiesterase 5: INSIGHTS INTO NUCLEOTIDE SPECIFICITY, DIMERIZATION, AND cGMP-DEPENDENT CONFORMATIONAL CHANGE J. Biol. Chem., August 15, 2008; 283(33): 22749 - 22759. [Abstract] [Full Text] [PDF]
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S. German-Retana, J. Walter, B. Doublet, G. Roudet-Tavert, V. Nicaise, C. Lecampion, M.-C. Houvenaghel, C. Robaglia, T. Michon, and O. Le Gall Mutational Analysis of Plant Cap-Binding Protein eIF4E Reveals Key Amino Acids Involved in Biochemical Functions and Potyvirus Infection J. Virol., August 1, 2008; 82(15): 7601 - 7612. [Abstract] [Full Text] [PDF]
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T. Ishibashi, K. So, C. G. Cupples, and J. Ausio MBD4-Mediated Glycosylase Activity on a Chromatin Template Is Enhanced by Acetylation Mol. Cell. Biol., August 1, 2008; 28(15): 4734 - 4744. [Abstract] [Full Text] [PDF]
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L. Michelet, M. Zaffagnini, H. Vanacker, P. Le Marechal, C. Marchand, M. Schroda, S. D. Lemaire, and P. Decottignies In Vivo Targets of S-Thiolation in Chlamydomonas reinhardtii J. Biol. Chem., August 1, 2008; 283(31): 21571 - 21578. [Abstract] [Full Text] [PDF]
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B. Bakrac, I. Gutierrez-Aguirre, Z. Podlesek, A. F.-P. Sonnen, R. J. C. Gilbert, P. Macek, J. H. Lakey, and G. Anderluh Molecular Determinants of Sphingomyelin Specificity of a Eukaryotic Pore-forming Toxin J. Biol. Chem., July 4, 2008; 283(27): 18665 - 18677. [Abstract] [Full Text] [PDF]
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J. Schwenk, G. Zolles, N. G. Kandias, I. Neubauer, H. Kalbacher, M. Covarrubias, B. Fakler, and D. Bentrop NMR Analysis of KChIP4a Reveals Structural Basis for Control of Surface Expression of Kv4 Channel Complexes J. Biol. Chem., July 4, 2008; 283(27): 18937 - 18946. [Abstract] [Full Text] [PDF]
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S. Han, H. Yi, S.-J. Yin, Z.-Y. Chen, H. Liu, Z.-J. Cao, Y.-L. Wu, and W.-X. Li Structural Basis of a Potent Peptide Inhibitor Designed for Kv1.3 Channel, a Therapeutic Target of Autoimmune Disease J. Biol. Chem., July 4, 2008; 283(27): 19058 - 19065. [Abstract] [Full Text] [PDF]
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S. Richter, A. Wenzel, M. Stein, R. R. Gabdoulline, and R. C. Wade webPIPSA: a web server for the comparison of protein interaction properties Nucleic Acids Res., July 1, 2008; 36(suppl_2): W276 - W280. [Abstract] [Full Text] [PDF]
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S. Montgomerie, J. A. Cruz, S. Shrivastava, D. Arndt, M. Berjanskii, and D. S. Wishart PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation Nucleic Acids Res., July 1, 2008; 36(suppl_2): W202 - W209. [Abstract] [Full Text] [PDF]
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A. M. Comeau and H. M. Krisch The Capsid of the T4 Phage Superfamily: The Evolution, Diversity, and Structure of Some of the Most Prevalent Proteins in the Biosphere Mol. Biol. Evol., July 1, 2008; 25(7): 1321 - 1332. [Abstract] [Full Text] [PDF]
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M.-H. Chang, J. DiPiero, F. D. Sonnichsen, and M. F. Romero Entry to "Formula Tunnel" Revealed by SLC4A4 Human Mutation and Structural Model J. Biol. Chem., June 27, 2008; 283(26): 18402 - 18410. [Abstract] [Full Text] [PDF]
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T. Tomo, Y. Kato, T. Suzuki, S. Akimoto, T. Okubo, T. Noguchi, K. Hasegawa, T. Tsuchiya, K. Tanaka, M. Fukuya, et al. Characterization of Highly Purified Photosystem I Complexes from the Chlorophyll d-dominated Cyanobacterium Acaryochloris marina MBIC 11017 J. Biol. Chem., June 27, 2008; 283(26): 18198 - 18209. [Abstract] [Full Text] [PDF]
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M. Yi, H. Tjong, and H.-X. Zhou Spontaneous conformational change and toxin binding in {alpha}7 acetylcholine receptor: Insight into channel activation and inhibition PNAS, June 17, 2008; 105(24): 8280 - 8285. [Abstract] [Full Text] [PDF]
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