Detection of trans–cis flips and peptide‐plane flips in protein structures. (1st August 2015)

• Record Type: Journal Article
• Authors: Touw, Wouter G.; Joosten, Robbie P.; Vriend, Gert
• Is Part Of: Acta crystallographica. Volume 71:Part 8(2015:Aug.)
• Page Start: 1604
• Page End: 1614
• Publication Date: 2015-08-01
• Subjects: Biomolecules -- Structure -- Periodicals; Physical biochemistry -- Periodicals; X-ray crystallography -- Periodicals; Crystallography -- Periodicals; 572
• DOI: 10.1107/S1399004715008263
• Languages: English
• ISSNs: 0907-4449

Abstract

<abstract abstract-type="main" xml:lang="en"> <title> <x xml:space="preserve">Abstract</x> </title> <p>A coordinate‐based method is presented to detect peptide bonds that need correction either by a peptide‐plane flip or by a <italic>trans</italic>–<italic>cis</italic> inversion of the peptide bond. When applied to the whole Protein Data Bank, the method predicts 4617 <italic>trans</italic>–<italic>cis</italic> 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 <italic>WHAT_CHECK</italic>.</p> </abstract>