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Protein structure homology modeling using SWISS-MODEL workspace

Nature Protocols volume 4, pages 1–13 (2009)Cite this article

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Abstract

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.

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Figure 1
Figure 2: Workflow of comparative protein structure modeling using SWISS-MODEL workspace.
Figure 3: Example of a personal user workspace.
Figure 4
Figure 5: Typical view of a SWISS-MODEL workspace result.
Figure 6: Target sequence annotation for the putative protein kinase C delta from Drosophila (PKC δ, UniProt AC: P83099).
Figure 7: Model of the kinase domain of the putative PKC δ from Drosophila shown as ribbon representation in DeepView colored from blue (N terminus) to red (C terminus).

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Change history

  • 30 July 2009

    The version of this article initially published indicated that only Torsten Schwede was affiliated with the Swiss Institute of Bioinformatics in addition to the Biozentrum, University of Basel, Basel, Switzerland. However, all six authors are affiliated with both the Biozentrum and the Swiss Institute of Bioinformatics. The error has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

We are grateful to Dr Michael Podvinec for his enthusiastic support and excellent coordination of the Scrum process for the SWISS-MODEL team. We are thankful for financial support of our group by the Swiss Institute of Bioinformatics (SIB).

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  1. Biozentrum, University of Basel, Klingelbergstrasse 50-70, Basel, CH 4056, Switzerland

    Lorenza Bordoli, Florian Kiefer, Konstantin Arnold, Pascal Benkert, James Battey & Torsten Schwede

  2. Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, Basel, CH 4056, Switzerland

    Lorenza Bordoli, Florian Kiefer, Konstantin Arnold, Pascal Benkert, James Battey & Torsten Schwede

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Bordoli, L., Kiefer, F., Arnold, K. et al. Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc 4, 1–13 (2009). https://doi.org/10.1038/nprot.2008.197

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