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Nucleic Acids Research Advance Access originally published online on May 3, 2007
Nucleic Acids Research 2007 35(Web Server issue):W403-W406; doi:10.1093/nar/gkm263
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W403-W406
© 2007 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.

Articles

NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures

Christian X. Weichenberger and Manfred J. Sippl*

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

*To whom correspondence should be addressed. Tel: +43 662 8044 5797; Fax: +43 662 8044 176; Email: sippl{at}came.sbg.ac.at

Received January 31, 2007. Revised March 30, 2007. Accepted April 8, 2007.

The current Protein Data Bank (PDB) contains about 40 000 protein structures with approximately half a million incorrect atom positions resulting from erroneously assigned asparagine (Asn) and glutamine (Gln) rotamers. These errors affect applications in protein structure analysis, modeling and docking and therefore the detection, correction and prevention of such errors is highly desirable. We present NQ-Flipper, a web service based on mean force potentials to automatically detect and correct erroneous Asn and Gln rotamers. The service accepts protein structure files formatted in PDB style or PDB codes. For an Asn/Gln side-chain amide NQ-Flipper computes the total interaction energy with the surrounding atoms as the sum of pairwise atom–atom interaction energies. The energy difference between the original and the alternative rotamers identifies the correct configuration of the amide group. The web service lists the interaction energies of all Asn/Gln residues found in a PDB file and shows the structure and offending residues in an interactive 3D viewer. The corrected protein structure is available for download in various compression formats. The web service is accessible at http://flipper.services.came.sbg.ac.at


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C. X. Weichenberger, P. Byzia, and M. J. Sippl
Visualization of unfavorable interactions in protein folds
Bioinformatics, May 1, 2008; 24(9): 1206 - 1207.
[Abstract] [Full Text] [PDF]


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