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The SWISS-MODEL expert system for comparative protein structure modeling

Research Project
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01.01.2000
 - 31.12.2025

SWISS-MODEL is a web-based expert system dedicated to protein structure homology modeling. Homology modeling is currently the most accurate method to generate reliable three-dimensional protein structure models and is routinely used in many practical applications. Homology (or comparative) modeling methods make use of experimental protein structures ("templates") to build models for evolutionary related proteins ("targets"). SWISS-MODEL is one of the most widely used web-based modeling servers with nearly one million model requests annually. The SWISS-MODEL Workspace provides a personal working environment where the user can carry out several modeling projects in parallel. The necessary resources, i.e. up-to-date protein sequence and structure databases and specialized tools for template selection, model building and structure quality evaluation are accessible using a web interface. Currently, the system supports more than 250'000 registered users. The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modeling pipeline. The aim of the SWISS-MODEL Repository is to provide access to an up-to-date collection of annotated 3D protein models for human proteins and a set of relevant models organisms. The Repository allows the users to assess the quality of the models in the database, search for alternative template structures, and to build models interactively via SWISS-MODEL Workspace. The SWISS-MODEL Repository is tightly integrated with external resources such as UniProt, InterPro and STRING databases. The services of the SWISS-MODEL expert system are available at http://swissmodel.expasy.org/ SWISS-MODEL is supported by the SIB Swiss Institute of Bioinformatics.

Collaborations & Cooperations

2011 - Participation or Organization of Collaborations on a national level
von Mering, Christian, University of Zürich, Exchange of methods

Publications

Bienert, Stefan et al. (2017) ‘The SWISS-MODEL Repository - new features and functionality’, Nucleic Acids Research, 45(D1), pp. D313–D319. Available at: https://doi.org/10.1093/nar/gkw1132.

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Biasini, Marco et al. (2014) ‘SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information’, Nucleic Acids Research, 42(Web Server issue), pp. W252–8. Available at: https://doi.org/10.1093/nar/gku340.

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Schmidt, Tobias, Bergner, Andreas and Schwede, Torsten (2014) ‘Modelling three-dimensional protein structures for applications in drug design’, Drug discovery today, 19(7), pp. 890–7. Available at: https://doi.org/10.1016/j.drudis.2013.10.027.

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Biasini, M et al. (2013) ‘OpenStructure : an integrated software framework for computational structural biology’, Acta crystallographica. Section D, Biological crystallography, 69(Pt 5), pp. 701–9. Available at: https://doi.org/10.1107/s0907444913007051.

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Schwede, Torsten (2013) ‘Protein modeling: what happened to the ‘protein structure gap’?’, Structure: with folding and design, 21(9), pp. 1531–1540. Available at: https://doi.org/10.1016/j.str.2013.08.007.

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Schwede, Torsten (2013) ‘Homology Modeling of Protein Structures’, Encyclopedia of Biophysics. Edited by Roberts, G.C.K. Berlin: Springer (Encyclopedia of Biophysics). Available at: https://doi.org/10.1007/978-3-642-16712-6_417.

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Barbato, Alessandro et al. (2012) ‘Improving your target-template alignment with MODalign’, Bioinformatics, 28(7), pp. 1038–9. Available at: https://doi.org/10.1093/bioinformatics/bts070.

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Bordoli, Lorenza and Schwede, Torsten (2012) ‘Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal’, in Orry, Andrew JW; Abagyan, Ruben (ed.) Homology Modeling: Methods and Protocols. New York, USA: Humana Press (Methods in Molecular Biology), p. S. 107–36. Available at: https://doi.org/10.1007/978-1-61779-588-6_5.

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Benkert, Pascal, Biasini, Marco and Schwede, Torsten (2011) ‘Toward the estimation of the absolute quality of individual protein structure models’, Bioinformatics, 27(3), pp. 343–50. Available at: https://doi.org/10.1093/bioinformatics/btq662.

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Haas, J. and Schwede, T. (2010) ‘Protein Homology Modelling - Providing Three-dimensional Models for Proteins where Experimental Data is Missing’, ERCIM News, 82, pp. 20–21. Available at: http://ercim-news.ercim.eu/images/stories/EN82/EN82-web.pdf.

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Bordoli, Lorenza et al. (2009) ‘Protein structure homology modelling using SWISS-MODEL Workspace’, Nature Protocols, 4(1), pp. 1–13. Available at: https://doi.org/10.1038/nprot.2008.197.

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Guex, Nicolas, Peitsch, Manuel C and Schwede, Torsten (2009) ‘Automated comparative protein structure modeling with Swiss-model and Swiss-PdbViewer : a historical perspective’, Electrophoresis, 30 Suppl 1(S1), pp. S162–73. Available at: https://doi.org/10.1002/elps.200900140.

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Kiefer, F. et al. (2009) ‘The Swiss-model Repository and associated resources’, Nucleic Acids Research, 37(1 Supplement), pp. D387–D392. Available at: https://doi.org/10.1093/nar/gkn750.

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Schwede, T. and Peitsch, M. C. (2009) ‘Protein Structure Modeling and Docking at the Swiss Institute of Bioinformatics’, in Appel, RD; Feytmans, E. (ed.) Bioinformatics. A Swiss Perspective. New Jersey: World Scientific (Bioinformatics. A Swiss Perspective), p. S. 219–246. Available at: https://doi.org/10.1142/9789812838780_0009.

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Schwede, T. et al. (2008) ‘Protein Structure Modeling’, in Schwede, T.; Peitsch, M.C. (ed.) Computational structural biology. Singapore: World Scientific (Computational structural biology), p. S. 700. Available at: https://doi.org/10.1142/9789812778789_0001.

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Arnold, Konstantin et al. (2006) ‘The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling’, Bioinformatics, 22(2), pp. 195–201. Available at: https://doi.org/10.1093/bioinformatics/bti770.

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Kopp, Jürgen and Schwede, Torsten (2006) ‘The Swiss-model Repository : new features and functionalities’, Nucleic Acids Research, 34(Database issue), pp. D315–8. Available at: https://doi.org/10.1093/nar/gkj056.

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Kopp, J. and Schwede, T. (2004) ‘The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models’, Nucleic Acids Research, 32(1 Supplement), pp. D230–D234. Available at: https://doi.org/10.1093/nar/gkh008.

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Kopp, Jurgen and Schwede, Torsten (2004) ‘Automated protein structure homology modeling : a progress report’, Pharmacogenomics, 5(4), pp. 405–16. Available at: https://doi.org/10.1517/14622416.5.4.405.

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Schwede, T. et al. (2003) ‘Swiss-model : an automated protein homology-modeling server’, Nucleic Acids Research, 31(13), pp. 3381–5. Available at: https://doi.org/10.1093/nar/gkg520.

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Peitsch, M.C. et al. (2002) ‘Protein homology modeling’, Nature encyclopedia of the human genome, 4.

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Kopp, J., Peitsch, M. C. and Schwede, T. (2002) ‘Protein Structure Modeling in Functional Genomics’, in Frontiers in Computational Genomics. Horizon Scientific Press: Horizon Scientific Press (Frontiers in Computational Genomics). Available at: http://books.google.com/books?id=hJ79LFI7f_IC&printsec=frontcover&dq=frontiers+in+computational+genomics#PPA89,M1.

URLs
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Peitsch, M C, Schwede, T and Guex, N (2000) ‘Automated protein modelling-the proteome in 3D’, Pharmacogenomics, 1(3), pp. 257–66. Available at: https://doi.org/10.1517/14622416.1.3.257.

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Schwede, T et al. (2000) ‘Protein structure computing in the genomic era’, Research in microbiology, 151(2), pp. 107–12. Available at: https://doi.org/10.1016/s0923-2508(00)00121-2.

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Guex, N., Schwede, T. and Peitsch, M. C. (2000) ‘Protein Tertiary Structure Modeling’, in Current Protocols in Protein Science. [New York]: Wiley (Current Protocols in Protein Science), p. 2.8.1–2.8.17. Available at: https://doi.org/10.1002/0471140864.ps0208s23.

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Members (6)

Profile Photo

Torsten Schwede

Principal Investigator
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Stefan Bienert

Project Member
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Lorenza Bordoli

Project Member
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Gabriel Studer

Project Member
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Gerardo Tauriello

Project Member
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Andrew Waterhouse

Project Member