Protocol

Homology Modeling

Volume 857 of the series Methods in Molecular Biology pp 107-136

Date:

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

  • Lorenza BordoliAffiliated withSIB Swiss Institute of Bioinformatics, Biozentrum University of Basel
  • , Torsten SchwedeAffiliated withSIB Swiss Institute of Bioinformatics, Biozentrum University of Basel Email author 

* Final gross prices may vary according to local VAT.

Get Access

Abstract

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