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Bioinformatics Advance Access published online on March 29, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn108
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Visualization of unfavorable interactions in protein folds

Christian X. Weichenberger 1, Piotr Byzia 2 and Manfred J. Sippl 1,*

1 Center of Applied Molecular Engineering, University of Salzburg, Hellbrunnerstrasse 34, 5020Salzburg, Austria

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


  Abstract

Summary: Three dimensional structures of proteins contain errors which often originate from limitations of the experimental techniques employed. Such errors frequently result in unfavorable atomic interactions. Here we present a new web service, called Interaction Viewer, for the visualization and correction of such errors. We show how the Interaction Viewer is used in combination with the NQ-Flipper service to spot strained asparagine and glutamine rotamers and we emphasize the convenience of this service in correcting such errors.

Availability: The web service is integrated with the NQ-Flipper service and accessible at http://flipper.services.came.sbg.ac.at

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

Associate Editor: Prof. Anna Tramontano

2Present Address: Institute of Physical and Theoretical Chemistry, Wrocøaw University ofTechnology, Wybrzeze Wyspianskiego 27, 50-370 Wrocøaw, Poland

Received on January 25, 2008; revised on March 10, 2008; accepted on March 23, 2008

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