Detection of trans–cis flips and peptide-plane flips in protein structures
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands)
- Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen (Netherlands)
A method is presented to detect peptide bonds that need either a trans–cis flip or a peptide-plane flip. 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.
- OSTI ID:
- 22389075
- Journal Information:
- Acta Crystallographica. Section D: Biological Crystallography, Vol. 71, Issue Pt 8; Other Information: PMCID: PMC4528797; PMID: 26249342; PUBLISHER-ID: kw5124; OAI: oai:pubmedcentral.nih.gov:4528797; Copyright (c) Touw et al. 2015; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA); ISSN 0907-4449
- Country of Publication:
- Denmark
- Language:
- English
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