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Welcome to CAME's NQ-Flipper home page. NQ-Flipper
recognizes unfavorable rotamers of Asn and Gln residues in protein
structures. This service is applicable to structures obtained from X-ray
crystallography, NMR or modeling studies. The method is based on
knowledge-based potentials of mean force compiled from a database of known
protein structures determined by X-ray crystallography. The potentials are
then refined by several cycles of rotamer correction and recompilation of
potentials. The refined potentials are used here to validate or correct
asparagine and glutamine amide rotamers.
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To identify and correct improper rotamers, enter the PDB four letter code
(e.g. 1ra9) or
upload your own PDB formatted file. Hitting the "Validate Structure"
button executes the program, displays the structure and highlights the
residues that need to be corrected. (Please have Java and JavaScript enabled
in your web browser.)
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Usually, there is no need to change any of the parameters. However, if you
want to explore your structure in more detail, please find a detailed
description of the parameters here.
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NQ-Flipper V2.7 has
quadrupled in speed and finally displays interactions
to crystal neighbors. You also benefit from this on your own machine,
simply download
the program.
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References
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Weichenberger, C. X., Byzia, P., and Sippl, M. J. (2008) Visualization of
unfavorable interactions in protein folds.
Bioinformatics., 24, 1206-1207.
[Abstract (HTML)]
[pdf]
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Weichenberger, C. X., and Sippl, M. J. (2007) Recognition and Correction of
Erroneous Asparagine and Glutamine Side Chain Rotamers in Protein Structures.
Nucleic Acids Res., 35(Web Server issue), W403-406.
[Abstract (HTML)]
[pdf]
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Weichenberger, C. X., and Sippl, M. J. (2006) NQ-Flipper: Validation and
Correction of Asparagine/Glutamine Amide Rotamers in Protein Crystal
Structures.
Bioinformatics, 22, 1397-1398.
[Abstract
(HTML)]
[pdf]
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Weichenberger, C. X., and Sippl, M. J. (2006) Self-consistent Assignment of
Asparagine and Glutamine Amide Rotamers in Protein Crystal
Structures.
Structure, 14, 967-972.
[Abstract
(HTML)]
[pdf]
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