{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T12:46:04Z","timestamp":1791895564400,"version":"4.3.4"},"reference-count":34,"publisher":"Wiley","issue":"11","license":[{"start":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:00:00Z","timestamp":1791849600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:00:00Z","timestamp":1791849600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100004189","name":"Max-Planck-Gesellschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004189","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Protein Science"],"published-print":{"date-parts":[[2026,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Non\u2010standard amino acids (ncAAs) together with synthetic additions (like caps and linkers) are of wide interest for protein design and pharmaceutical optimization, as they can improve physicochemical properties and possibly reshape protein structure. Their inclusion in experimental structures has not been explored systematically. It remains elusive which components are those most impactful for protein design. We therefore collected all non\u2010standard components present in the Protein Data Bank (PDB) into MONDE\u00b7T: A database of 1,210 unique ncAAs and 724 other synthetic components present in 23,149 PDB structures with a corresponding webserver. Analyses can focus on a single component or a single structure, illustrated here by example applications. MONDE\u00b7T allows for download of the data, visualization of a structure, identification of unusual backbone angles, and comparison of chemical similarities. The webserver is hosted at the Max Planck Institute T\u00fcbingen, accessible online via\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/mondet.tuebingen.mpg.de\/\">https:\/\/mondet.tuebingen.mpg.de\/<\/jats:ext-link>\n                    . MONDE\u00b7T is freely available under the Creative Commons 4.0 License.\n                  <\/jats:p>","DOI":"10.1002\/pro.70809","type":"journal-article","created":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T11:52:39Z","timestamp":1791892359000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["<scp>MONDE<\/scp>\n                    \u00b7T: A database and interactive webserver for non\u2010standard amino acids and peptide components in the\n                    <scp>PDB<\/scp>"],"prefix":"10.1002","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-9721-4265","authenticated-orcid":false,"given":"Alex","family":"Waldherr","sequence":"first","affiliation":[{"name":"Department for Protein Evolution Max Planck Institute for Biology  T\u00fcbingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-4448-9831","authenticated-orcid":false,"given":"Gesa L.","family":"Freimann","sequence":"additional","affiliation":[{"name":"Department for Protein Evolution Max Planck Institute for Biology  T\u00fcbingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrei N.","family":"Lupas","sequence":"additional","affiliation":[{"name":"Department for Protein Evolution Max Planck Institute for Biology  T\u00fcbingen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,13]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.51.5.786"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0969-2126(01)00224-6"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/nsb1203-980"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2023.167994"},{"issue":"1","key":"e_1_2_9_6_1","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/S0021-9258(19)52289-X","article-title":"Conversion of phosphorylase b to phosphorylase a in muscle extracts","volume":"216","author":"Fisher EH","year":"1955","journal-title":"J Biol Chem"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1042\/bj0640323"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.200300777"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks991"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja104616z"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.282.5393"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1002\/j.1460-2075.1990.tb08287.x"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad1090"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1002\/tera.1420230311"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04868-x"},{"key":"e_1_2_9_16_1","unstructured":"LandrumGand contributors.RDKit Open\u2010source toolkit for cheminformatics.https:\/\/www.rdkit.org2006."},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.5b00726"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/331723a0"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt0808-864"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1962210"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/0163-7827(88)90012-4"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.7b08402"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/s0022-2836(63)80023-6"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2020.11.003"},{"key":"e_1_2_9_25_1","first-page":"189","volume-title":"Nichtproteinstrukturkomponenten: Polysaccharide","author":"Schellenberger A","year":"1989"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab314"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1069588"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.270.11.6163"},{"key":"e_1_2_9_29_1","unstructured":"SunH.Molstar Viewer into Dash.2023."},{"key":"e_1_2_9_30_1","unstructured":"TanimotoT.An elementary mathematical theory of classification and prediction. 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