{"doi":"10.1002/prot.10320","title":"<scp>D</scp>‐amino acid residues in peptides and proteins","abstract":"<jats:title>Abstract</jats:title><jats:p>We have investigated the <jats:sc>D</jats:sc>‐amino acid residues present in Protein Data Bank (PDB) entries, categorizing them into “real” <jats:sc>D</jats:sc>‐residues and artifacts. In polypeptide chains of more than 20 residues, only a single instance of a “real” <jats:sc>D</jats:sc>‐residue, other than those deliberately designed or engineered, was found. This example was the result of a slow chemical epimerization process. Another 12 designed <jats:sc>D</jats:sc>‐residues were found in these longer polypeptide chains. Smaller peptides of 20 or fewer residues contained 479 “real” <jats:sc>D</jats:sc>‐residues, the majority in various gramicidin, actinomycin, or cyclosporin structures. We found 148 PDB entries with “real” <jats:sc>D</jats:sc>‐residues and a further 186, in which all apparent <jats:sc>D</jats:sc>‐residues are artifacts. Investigating the (ϕ, ψ) preferences of the “real” <jats:sc>D</jats:sc>‐residues, we found that the region around (−60°, −45°) was almost completely unoccupied, even though it is not formally disallowed. We link the low propensity to occupy this region with the α‐helix destabilizing properties of <jats:sc>D</jats:sc>‐residues. Proteins 2003;50:563–571. © 2003 Wiley‐Liss, Inc.</jats:p>","journal":"Proteins: Structure, Function, and Bioinformatics","year":2003,"id":15406,"datarank":3.2879741353680076,"base_score":4.110873864173311,"endowment":4.110873864173311,"self_citation_contribution":0.6166310796259968,"citation_network_contribution":2.671343055742011,"self_endowment_contribution":0.6166310796259968,"citer_contribution":2.671343055742011,"corpus_percentile":null,"corpus_rank":null,"citation_count":60,"citer_count":60,"citers_with_citation_signal":52,"citers_with_endowment":52,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":95934,"name":"James Smith","orcid":null,"position":1,"is_corresponding":false},{"id":117662,"name":"John B.O. Mitchell","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":4.110873864173311,"endowment":4.110873864173311,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"12577262","pmcid":null,"openalex_id":"https://openalex.org/W2171014201","authors":[],"funders":[],"total_grants":0,"fwci":1.6034,"citation_percentile":0.82860638,"influential_citations":5,"citation_trend":[{"year":2012,"count":5},{"year":2013,"count":2},{"year":2014,"count":1},{"year":2015,"count":2},{"year":2016,"count":1},{"year":2017,"count":3},{"year":2018,"count":1},{"year":2019,"count":2},{"year":2020,"count":3},{"year":2021,"count":2},{"year":2022,"count":1},{"year":2023,"count":1},{"year":2024,"count":4},{"year":2025,"count":1},{"year":2026,"count":1}],"oa_status":"closed","license":"http://onlinelibrary.wiley.com/termsAndConditions#vor","oa_locations":[{"url":"https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fprot.10320","host_type":"publisher"},{"url":"https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.10320","host_type":"publisher"},{"url":"https://doi.org/10.1002/prot.10320","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/12577262","host_type":"repository"}],"fields_of_study":["Protein Structure and Dynamics","Advanced Proteomics Techniques and Applications","Chemical Synthesis and Analysis","Chemistry","Medicine","Biology","Amino Acids","Artifacts","Crystallography, X-Ray","Cyclosporine","Dactinomycin","Databases, Protein","Gramicidin","Melitten","Molecular Structure","Nuclear Magnetic Resonance, Biomolecular","Peptides","Protein Structure, Secondary","Proteins","Stereoisomerism"],"mesh_terms":["Amino Acids","Dactinomycin","Gramicidin","Melitten","Peptides","Proteins","Stereoisomerism","Molecular Structure","Artifacts","Cyclosporine","Protein Structure, Secondary","Crystallography, X-Ray","Nuclear Magnetic Resonance, Biomolecular","Databases, Protein"],"keywords":["Protein Data Bank (RCSB PDB)","Residue (chemistry)","Amino acid residue","Chemistry","Protein Data Bank","Epimer","Stereochemistry","Peptide","Amino acid","Protein structure","Peptide sequence","Biochemistry"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-01T17:34:57.607215Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}