Protocol abstract

Nature Protocols 4, 1 - 13 (2009)
Published online: 11 December 2008 | Corrected online: 30 July 2009 | doi:10.1038/nprot.2008.197

Subject Categories: Biochemistry and protein analysis | Computational and theoretical biology

Protein structure homology modeling using SWISS-MODEL workspace

Lorenza Bordoli1,2, Florian Kiefer1,2, Konstantin Arnold1,2, Pascal Benkert1,2, James Battey1,2 & Torsten Schwede1,2

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.

  1. Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH 4056 Basel, Switzerland.
  2. SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH 4056 Basel, Switzerland.

Correspondence to: Torsten Schwede1,2 e-mail: