{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T15:16:01Z","timestamp":1776006961987,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1011895","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,7,30]],"date-time":"2024-07-30T00:00:00Z","timestamp":1722297600000}}],"reference-count":69,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2024,6,24]],"date-time":"2024-06-24T00:00:00Z","timestamp":1719187200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"NIAID","doi-asserted-by":"crossref","award":["U19AI117905, R01AI11386, 1UM1 AI100663, and UM1 AI144462"],"award-info":[{"award-number":["U19AI117905, R01AI11386, 1UM1 AI100663, and UM1 AI144462"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1141162"],"award-info":[{"award-number":["OPP1141162"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"name":"BMGF CAVD"},{"name":"NIH","award":["1P01AI167966 and P50AI150464"],"award-info":[{"award-number":["1P01AI167966 and P50AI150464"]}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1156262"],"award-info":[{"award-number":["OPP1156262"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014895","name":"Open Philanthropy Project","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014895","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"NIAID","doi-asserted-by":"crossref","award":["T32AI007244"],"award-info":[{"award-number":["T32AI007244"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NIH","award":["R01-GM127278"],"award-info":[{"award-number":["R01-GM127278"]}]},{"name":"NIH\/NIGMS","award":["R35 GM122517"],"award-info":[{"award-number":["R35 GM122517"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Carbohydrates and glycoproteins modulate key biological functions. However, experimental structure determination of sugar polymers is notoriously difficult. Computational approaches can aid in carbohydrate structure prediction, structure determination, and design. In this work, we developed a glycan-modeling algorithm, <jats:italic>GlycanTreeModeler<\/jats:italic>, that computationally builds glycans layer-by-layer, using adaptive kernel density estimates (KDE) of common glycan conformations derived from data in the Protein Data Bank (PDB) and from quantum mechanics (QM) calculations. <jats:italic>GlycanTreeModeler<\/jats:italic> was benchmarked on a test set of glycan structures of varying lengths, or \u201ctrees\u201d. Structures predicted by <jats:italic>GlycanTreeModeler<\/jats:italic> agreed with native structures at high accuracy for both <jats:italic>de novo<\/jats:italic> modeling and experimental density-guided building. We employed these tools to design <jats:italic>de novo<\/jats:italic> glycan trees into a protein nanoparticle vaccine to shield regions of the scaffold from antibody recognition, and experimentally verified shielding. This work will inform glycoprotein model prediction, glycan masking, and further aid computational methods in experimental structure determination and refinement.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1011895","type":"journal-article","created":{"date-parts":[[2024,6,24]],"date-time":"2024-06-24T19:35:57Z","timestamp":1719257757000},"page":"e1011895","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":10,"title":["Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8586-1907","authenticated-orcid":true,"given":"Jared","family":"Adolf-Bryfogle","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jason W.","family":"Labonte","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John C.","family":"Kraft","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maxim","family":"Shapovalov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sebastian","family":"Raemisch","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"L\u00fctteke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frank","family":"DiMaio","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher D.","family":"Bahl","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jesper","family":"Pallesen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Neil P.","family":"King","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey J.","family":"Gray","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel W.","family":"Kulp","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William R.","family":"Schief","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2024,6,24]]},"reference":[{"key":"pcbi.1011895.ref001","doi-asserted-by":"crossref","DOI":"10.1002\/9783527618255","volume-title":"Carbohydrates in Chemistry and Biology","author":"B Ernst","year":"2000","edition":"1"},{"issue":"5361","key":"pcbi.1011895.ref002","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1126\/science.280.5361.248","article-title":"Viral Strategies of Immune Evasion.","volume":"280","author":"HL Ploegh","year":"1998","journal-title":"Science"},{"issue":"6059","key":"pcbi.1011895.ref003","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1126\/science.1213256","article-title":"A Potent and Broad Neutralizing Antibody Recognizes and Penetrates the HIV Glycan Shield","volume":"334","author":"R Pejchal","year":"2011","journal-title":"Science"},{"issue":"5","key":"pcbi.1011895.ref004","doi-asserted-by":"crossref","first-page":"e1003342","DOI":"10.1371\/journal.ppat.1003342","article-title":"Broadly Neutralizing Antibody PGT121 Allosterically Modulates CD4 Binding via Recognition of the HIV-1 gp120 V3 Base and Multiple Surrounding Glycans.","volume":"9","author":"JP Julien","year":"2013","journal-title":"PLoS Pathog"},{"issue":"5","key":"pcbi.1011895.ref005","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1016\/j.immuni.2014.04.009","article-title":"Broadly Neutralizing HIV Antibodies Define a Glycan-Dependent Epitope on the Prefusion Conformation of gp41 on Cleaved Envelope Trimers","volume":"40","author":"E Falkowska","year":"2014","journal-title":"Immunity"},{"issue":"5512","key":"pcbi.1011895.ref006","doi-asserted-by":"crossref","first-page":"2376","DOI":"10.1126\/science.1058714","article-title":"Glycosylation of Nucleocytoplasmic Proteins: Signal Transduction and O-GlcNAc","volume":"291","author":"L. 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