Open AccessDetection of trans – cis flips and peptide‐plane flips in protein structures
Author(s) -
Touw Wouter G.,
Joosten Robbie P.,
Vriend Gert
Publication year - 2015
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s1399004715008263
Subject(s) - peptide , plane (geometry) , protein data bank , algorithm , computer science , geometry , physics , geodesy , mathematics , protein structure , geology , nuclear magnetic resonance
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 .