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Nucleic Acids Research, 2004, Vol. 32, Database issue D230-D234
© 2004 Oxford University Press

The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models

Jürgen Kopp and Torsten Schwede*

Biozentrum der Universität Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50–70, CH 4056 Basel, Switzerland

*To whom correspondence should be addressed. Tel: +41 61 267 15 81; Fax: +41 61 267 15 84; Email: torsten.schwede{at}unibas.ch

The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL. The Repository currently contains about 300 000 three-dimensional models for sequences from the Swiss-Prot and TrEMBL databases. The content of the Repository is updated on a regular basis incorporating new sequences, taking advantage of new template structures becoming available and reflecting improvements in the underlying modelling algorithms. Each entry consists of one or more three-dimensional protein models, the superposed template structures, the alignments on which the models are based, a summary of the modelling process and a force field based quality assessment. The SWISS-MODEL Repository can be queried via an interactive website at http://swissmodel.expasy. org/repository/. Annotation and cross-linking of the models with other databases, e.g. Swiss-Prot on the ExPASy server, allow for seamless navigation between protein sequence and structure information. The aim of the SWISS-MODEL Repository is to provide access to an up-to-date collection of annotated three-dimensional protein models generated by automated homology modelling, bridging the gap between sequence and structure databases.


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