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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.

SUBMITTER: Touw WG

PROVIDER: S-EPMC4528797 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature

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Detection of trans-cis flips and peptide-plane flips in protein structures.

Touw Wouter G WG Joosten Robbie P RP Vriend Gert G

Acta crystallographica. Section D, Biological crystallography 20150728 Pt 8

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 ma ...[more]

PMID: 26249342

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