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Bioinformatics Advance Access originally published online on November 13, 2005
Bioinformatics 2006 22(2):195-201; doi:10.1093/bioinformatics/bti770
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

Konstantin Arnold 1,2, Lorenza Bordoli 1,2, Jürgen Kopp 1,2 and Torsten Schwede 1,2,*

1Biozentrum Basel, University of Basel Switzerland
2Swiss Institute of Bioinformatics Basel, Switzerland

*To whom correspondence should be addressed.

Motivation: Homology models of proteins are of great interest for planning and analysing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all required tools, programs and databases into a single web-based workspace facilitates access to homology modelling from a computer with web connection without the need of downloading and installing large program packages and databases.

Results: SWISS-MODEL workspace is a web-based integrated service dedicated to protein structure homology modelling. It assists and guides the user in building protein homology models at different levels of complexity. A personal working environment is provided for each user where several modelling projects can be carried out in parallel. Protein sequence and structure databases necessary for modelling are accessible from the workspace and are updated in regular intervals. Tools for template selection, model building and structure quality evaluation can be invoked from within the workspace. Workflow and usage of the workspace are illustrated by modelling human Cyclin A1 and human Transmembrane Protease 3.

Availability: The SWISS-MODEL workspace can be accessed freely at http://swissmodel.expasy.org/workspace/

Contact: Torsten.Schwede{at}unibas.ch

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on August 25, 2005; revised on November 7, 2005; accepted on November 7, 2005

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