Detection of trans-cis flips and peptide-plane flips in protein structures
SourceActa Crystallographica Section D-Biological Crystallography, 71, Pt 8, (2015), pp. 1604-14
Article / Letter to editor
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Acta Crystallographica Section D-Biological Crystallography
iss. Pt 8
SubjectRadboudumc 19: Nanomedicine RIMLS: Radboud Institute for Molecular Life Sciences
A coordinate-based method is presented to detect peptide bonds that need correction either by a peptide-plane flip or by a trans-cis inversion of the peptide bond. When applied to the whole Protein Data Bank, the method predicts 4617 trans-cis flips and many thousands of hitherto unknown peptide-plane flips. A few examples are highlighted for which a correction of the peptide-plane geometry leads to a correction of the understanding of the structure-function relation. All data, including 1088 manually validated cases, are freely available and the method is available from a web server, a web-service interface and through WHAT_CHECK.
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