The SWISS-MODEL expert system for comparative protein structure modeling
Project funded by own resources
Project title The SWISS-MODEL expert system for comparative protein structure modeling
Principal Investigator(s) Schwede, Torsten
Project Members Bordoli, Lorenza
Arnold, Konstantin
Haas, Jürgen
Waterhouse, Andrew
Bienert, Stefan
Studer, Gabriel
Bertoni, Martino
Tauriello, Gerardo
de Beer, Tjaart
Organisation / Research unit Departement Biozentrum / Bioinformatics (Schwede)
Project Website http://swissmodel.expasy.org
Project start 01.01.2000
Probable end 31.12.2020
Status Active
Abstract

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.

Keywords protein structure, comparative modeling, computational structural biology
Financed by University funds
Other funds

Published results ()

  ID Autor(en) Titel ISSN / ISBN Erschienen in Art der Publikation
50374  Kopp, Juergen; Schwede, Torsten  The SWISS-MODEL repository: new features and functionalities  0305-1048  NUCLEIC ACIDS RESEARCH  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
51133  Arnold, K; Bordoli, L; Kopp, J; Schwede, T  The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling  1367-4803  BIOINFORMATICS  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
54086  Kopp, J; Schwede, T  The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models  0305-1048  NUCLEIC ACIDS RESEARCH  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
54748  Schwede, T; Kopp, J; Guex, N; Peitsch, MC  SWISS-MODEL: an automated protein homology-modeling server  0305-1048  NUCLEIC ACIDS RESEARCH  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156342  Schwede, T.; Peitsch, M. C.  Protein Structure Modeling and Docking at the Swiss Institute of Bioinformatics  978-981-283-877-3 ; 981-283-877-5  Bioinformatics. A Swiss Perspective  Publication: Book Item (Buchkap., Lexikonartikel, jur. Kommentierung, Beiträge in Sammelbänden etc.) 
156344  Schwede, T.; Sali, A.; Eswar, N.; Peitsch, M. C.  Protein Structure Modeling  978-981-277-877-2 (hardcover : alk. paper) ; 981-277-877-2 (hardcover : alk. paper)  Computational structural biology  Publication: Book Item (Buchkap., Lexikonartikel, jur. Kommentierung, Beiträge in Sammelbänden etc.) 
156345  Kopp, J.; Peitsch, M. C.; Schwede, T.  Protein Structure Modeling in Functional Genomics  0954246446  Frontiers in Computational Genomics  Publication: Book Item (Buchkap., Lexikonartikel, jur. Kommentierung, Beiträge in Sammelbänden etc.) 
156346  Guex, N.; Schwede, T.; Peitsch, M. C.  Protein Tertiary Structure Modeling    Current Protocols in Protein Science  Publication: Book Item (Buchkap., Lexikonartikel, jur. Kommentierung, Beiträge in Sammelbänden etc.) 
156354  Guex, Nicolas; Peitsch, Manuel C; Schwede, Torsten  Automated comparative protein structure modeling with Swiss-model and Swiss-PdbViewer : a historical perspective  0173-0835  Electrophoresis  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156356  Bordoli, Lorenza; Kiefer, Florian; Arnold, Konstantin; Benkert, Pascal; Battey, James; Schwede, Torsten  Protein structure homology modelling using SWISS-MODEL Workspace  1754-2189  Nature Protocols  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156361  Kiefer, F.; Arnold, K.; Kunzli, M.; Bordoli, L.; Schwede, T.  The Swiss-model Repository and associated resources  0305-1048 ; 1362-4962  Nucleic Acids Research  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156372  Arnold, Konstantin; Bordoli, Lorenza; Kopp, Jürgen; Schwede, Torsten  The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling  1367-4803  Bioinformatics  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156373  Kopp, J.; Schwede, T.  The Swiss-model Repository : new features and functionalities  0305-1048 ; 1362-4962  Nucleic Acids Research  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156374  Kopp, Jurgen; Schwede, Torsten  Automated protein structure homology modeling : a progress report  0960-314X  Pharmacogenomics  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156375  Kopp, J.; Schwede, T.  The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models  0305-1048 ; 1362-4962  Nucleic Acids Research  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156378  Schwede, T.; Kopp, J.; Guex, N.; Peitsch, M. C.  Swiss-model : an automated protein homology-modeling server  0305-1048 ; 1362-4962  Nucleic Acids Research  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156381  Peitsch, M C; Schwede, T; Guex, N  Automated protein modelling-the proteome in 3D    Pharmacogenomics  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156382  Schwede, T; Diemand, A; Guex, N; Peitsch, M C  Protein structure computing in the genomic era  0923-2508  Research in microbiology  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156387  Peitsch, M.C.; Schwede, T.; Diemand, A.; Guex, N.  Protein homology modeling    Nature encyclopedia of the human genome  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
491038  Haas, J.; Schwede, T.  Protein Homology Modelling - Providing Three-dimensional Models for Proteins where Experimental Data is Missing  0926-4981  ERCIM News  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
749244  Benkert, Pascal; Biasini, Marco; Schwede, Torsten  Toward the estimation of the absolute quality of individual protein structure models  1367-4803  Bioinformatics  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
1141161  Barbato, Alessandro; Benkert, Pascal; Schwede, Torsten; Tramontano, Anna; Kosinski, Jan  Improving your target-template alignment with MODalign  1367-4811  Bioinformatics  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
1141171  Bordoli, Lorenza; Schwede, Torsten  Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal  978-1-61779-587-9  Homology Modeling: Methods and Protocols  Publication: Book Item (Buchkap., Lexikonartikel, jur. Kommentierung, Beiträge in Sammelbänden etc.) 
1596772  Schwede, Torsten  Homology Modeling of Protein Structures  978-3-642-16711-9 ; 978-3-642-16712-6  Encyclopedia of Biophysics  Publication: Book Item (Buchkap., Lexikonartikel, jur. Kommentierung, Beiträge in Sammelbänden etc.) 
1747788  Biasini, M; Schmidt, T; Bienert, S; Mariani, V; Studer, G; Haas, J; Johner, N; Schenk, A D; Philippsen, A; Schwede, T  OpenStructure : an integrated software framework for computational structural biology  0907-4449  Acta crystallographica. Section D, Biological crystallography  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
2158293  Schwede, Torsten  Protein modeling: what happened to the "protein structure gap"?  0969-2126  Structure: with folding and design  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
2188782  Uda, Narasimha Rao; Upert, Grégory; Angelici, Gaetano; Nicolet, Stefan; Schmidt, Tobias; Schwede, Torsten; Creus, Marc  Zinc-selective inhibition of the promiscuous bacterial amide-hydrolase DapE : implications of metal heterogeneity for evolution and antibiotic drug design  1756-5901  Metallomics  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
2261956  Schmidt, Tobias; Bergner, Andreas; Schwede, Torsten  Modelling three-dimensional protein structures for applications in drug design  1359-6446  Drug discovery today  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
3676032  Bienert, Stefan; Waterhouse, Andrew; de Beer, Tjaart A. P.; Tauriello, Gerardo; Studer, Gabriel; Bordoli, Lorenza; Schwede, Torsten  The SWISS-MODEL Repository - new features and functionality  0305-1048 ; 1362-4962  Nucleic Acids Research  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
2562978  Biasini, Marco; Bienert, Stefan; Waterhouse, Andrew; Arnold, Konstantin; Studer, Gabriel; Schmidt, Tobias; Kiefer, Florian; Cassarino, Tiziano Gallo; Bertoni, Martino; Bordoli, Lorenza; Schwede, Torsten  SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information  0305-1048 ; 1362-4962  Nucleic Acids Research  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 

Cooperations ()

  ID Kreditinhaber Kooperationspartner Institution Laufzeit - von Laufzeit - bis
105150  Schwede, Torsten  von Mering, Christian  University of Zürich  01.01.2009  31.12.2011 
   

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