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Bioinformatics Advance Access published online on January 2, 2008
Bioinformatics, doi:10.1093/bioinformatics/btm622
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

A Note on Difficult Structure Alignment Problems

Manfred J. Sippl * and Markus Wiederstein

Center of Applied Molecular Engineering, Division of Bioinformatics, Department of Molecular Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria

*To whom correspondence should be addressed. Prof. Manfred J. Sippl, E-mail: sippl{at}came.sbg.ac.at


  Abstract

Summary: Progress in structural biology depends on several key technologies. In particular tools for alignment and superposition of protein structures are indispensable. Here we describe the use of the TopMatch web service, an effective computational tool for protein structure alignment, for the visualization of structural similarities, and for highlighting relationships found in protein classifications. We provide several instructive examples.

Availability: TopMatch is available as a public web service at http://services.came.sbg.ac.at.

Contact: sippl{at}came.sbg.ac.at

Associate Editor: Prof. Burkhard Rost

Received on November 23, 2007; revised on December 12, 2007; accepted on December 13, 2007

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