Bioinformatics Advance Access published online on November 13, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti770
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1 Biozentrum Basel, University Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
* To whom correspondence should be addressed.
Motivation: Homology models of proteins are of great interest for planning and analyzing 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/.
Received August 25, 2005
Revised November 7, 2005
Accepted November 7, 2005
Article
The SWISS-MODEL Workspace: a web-based environment for protein structure homology modelling
Konstantin Arnold 1,
Lorenza Bordoli 1,
Jürgen Kopp 1,
and
Torsten Schwede 1 *
Torsten Schwede, E-mail: Torsten.Schwede{at}unibas.ch
Abstract 
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K. Michelsen, V. Schmid, J. Metz, K. Heusser, U. Liebel, T. Schwede, A. Spang, and B. Schwappach Novel cargo-binding site in the {beta} and {delta} subunits of coatomer J. Cell Biol., October 22, 2007; 179(2): 209 - 217. [Abstract] [Full Text] [PDF]
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H. Matta, L. Mazzacurati, S. Schamus, T. Yang, Q. Sun, and P. M. Chaudhary Kaposi's Sarcoma-associated Herpesvirus (KSHV) Oncoprotein K13 Bypasses TRAFs and Directly Interacts with the I{kappa}B Kinase Complex to Selectively Activate NF-{kappa}B without JNK Activation J. Biol. Chem., August 24, 2007; 282(34): 24858 - 24865. [Abstract] [Full Text] [PDF]
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 D. J. Scott, T. N. Wilkinson, S. Zhang, T. Ferraro, J. D. Wade, G. W. Tregear, and R. A. D. Bathgate Defining the LGR8 Residues Involved in Binding Insulin-Like Peptide 3 Mol. Endocrinol., July 1, 2007; 21(7): 1699 - 1712. [Abstract] [Full Text] [PDF]
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K. C. Cole, H. W. McLaughlin, and D. I. Johnson Use of Bimolecular Fluorescence Complementation To Study In Vivo Interactions between Cdc42p and Rdi1p of Saccharomyces cerevisiae Eukaryot. Cell, March 1, 2007; 6(3): 378 - 387. [Abstract] [Full Text] [PDF]
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