ArticleActa crystallographica. Section D, Biological crystallography2015
Detection of trans-cis flips and peptide-plane flips in protein structures.
Article in Acta crystallographica. Section D, Biological crystallography, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Defining the Active Conformation of Typical Protein Kinase Domains from Substrate-Bound PDB Structures Enables Active-State AlphaFold2 Models for All 437 Human Catalytic Protein Kinases.bioRxiv : the preprint server for biology · 2026Article
- Cis-nonProline peptides: Genuine occurrences and their functional roles.Protein science : a publication of the Protein Society · 2025Article
- Distance-based global analysis of consistentHeliyon · 2023Article
- Molecular-dynamics simulation methods for macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2023Article
- Backbone N-Amination Promotes the Folding of β-Hairpin Peptides via a Network of Hydrogen Bonds.Journal of chemical information and modeling · 2022Article
- Molecular Recognition of Lipid II by Lantibiotics: Synthesis and Conformational Studies of Analogues of Nisin and Mutacin Rings A and B.The Journal of organic chemistry · 2019Article
- Defining a new nomenclature for the structures of active and inactive kinases.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.Acta crystallographica. Section D, Structural biology · 2018Article
- Sixty-five years of the long march in protein secondary structure prediction: the final stretch?Briefings in bioinformatics · 2018Article
- An allosteric binding site of the α7 nicotinic acetylcholine receptor revealed in a humanized acetylcholine-binding protein.The Journal of biological chemistry · 2018Article
- Stereochemistry and Validation of Macromolecular Structures.Methods in molecular biology (Clifton, N.J.) · 2017Review
- Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation.Methods in enzymology · 2016Review
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3 authors.
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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.
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