title: Detection of trans-cis flips and peptide-plane flips in protein structures.
abstract: 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.
authors.affiliation: Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands.
authors.forename: Wouter G
authors.initials: WG
authors.lastname: Touw
authors.affiliation: Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Robbie P
authors.initials: RP
authors.lastname: Joosten
authors.affiliation: Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands.
authors.forename: Gert
authors.initials: G
authors.lastname: Vriend
mesh_terms: D000818:Animals; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D006801:Humans; D007168:IMP Dehydrogenase / Q000737:chemistry; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D020695:rab4 GTP-Binding Proteins / Q000737:chemistry
chemical_list: D010455:Peptides; D011506:Proteins; D007168:IMP Dehydrogenase; C501687:IMPDH2 protein, human; D020695:rab4 GTP-Binding Proteins
keywords: cis peptide bond; peptide conformation; structure correction; structure validation