The SWISS-MODEL Repository: new features and functionalities

Abstract

The SWISS-MODEL Repository is a database of annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline. As of September 2005, the repository contained 675,000 models for 604,000 different protein sequences of the UniProt database. Regular updates ensure that the content of the repository reflects the current state of sequence and structure databases, integrating new or modified target sequences, and making use of new template structures. Each Repository entry consists of one or more 3D models accompanied by detailed information about the target protein and the model building process: functional annotation, a detailed template selection log, target-template alignment, summary of the model building and model quality assessment. The SWISS-MODEL Repository is freely accessible at http://swissmodel.expasy.org/repository/.

Figure 1

SWISS-MODEL Repository entry for Cyclodextrin glucanotransferase from Bacillus stearothermophilus (UniProt: Q9ZAQ0). (a) The ‘Model Info’ section provides a description of the template structure, the target-template alignment and a log of the modelling process. (b) Annotation of functional sites and individual domains of the target protein using InterPro assignments. (c) Structure of the model as ribbon representation using DeepView/PovRay coloured according to InterPro assignments. (d) Model quality evaluation are provided as Anolea and Gromos plots.