Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal

  • Lorenza Bordoli
  • Torsten SchwedeEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 857)


Comparative protein structure modeling is a computational approach to build three-dimensional structural models for proteins using experimental structures of related protein family members as templates. Regular blind assessments of modeling accuracy have demonstrated that comparative protein structure modeling is currently the most reliable technique to model protein structures. Homology models are often sufficiently accurate to substitute for experimental structures in a wide variety of applications. Since the usefulness of a model for specific application is determined by its accuracy, model quality estimation is an essential component of protein structure prediction. Comparative protein modeling has become a routine approach in many areas of life science research since fully automated modeling systems allow also nonexperts to build reliable models. In this chapter, we describe practical approaches for automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal.

Key words

Protein structure prediction Molecular models Automation Homology modeling Comparative modeling Quality estimation SWISS-MODEL Protein Model Portal QMEAN 



The authors thank Konstantin Arnold for his dedicated support of the SWISS-MODEL service, Jürgen Haas for his commitment to new developments in PMP, and all members of the group for fruitful discussions.

Funding: The development and operation of SWISS-MODEL was supported by the SIB Swiss Institute of Bioinformatics; The PMP of the Nature PSI Structural Biology Knowledgebase was supported by the National Institutes of Health NIH as a subgrant with Rutgers University, under Prime Agreement Award Numbers: 3U54GM074958-04S2 and 1U01 GM093324-01.


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© Springer Science+Business Media,LLC 2011

Authors and Affiliations

  1. 1.SIB Swiss Institute of BioinformaticsBiozentrum University of BaselBaselSwitzerland

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