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Bioinformatics Advance Access published online on April 4, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl128
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received January 12, 2006
Revised March 6, 2006
Accepted March 30, 2006

Applications note

NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures

Christian X. Weichenberger 1 and Manfred J. Sippl 1 *

1 Center of Applied Molecular Engineering, University of Salzburg, Jakob Haringerstraße 5, 5020 Salzburg, Austria

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


  Abstract

Summary: The error rate of asparagine (Asn) and glutamine (Gln) amide rotamers in protein crystal structures is in the order of 20% and as a consequence the current protein data base (PDB) contains approximately half a million incorrect Asn and Gln side-chain rotamers. Here we present NQ-Flipper, a web service based on knowledge-based potentials of mean force to automatically detect and correct erroneous rotamers. We achieve excellent agreement with expert curated data.

Availability: The program is accessible freely as a web service at http://flipper.services.came.sbg.ac.at.

Associate Editor: Anna Tramontano
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