{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T06:15:45Z","timestamp":1780553745703,"version":"3.54.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2019,12,16]],"date-time":"2019-12-16T00:00:00Z","timestamp":1576454400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-1707207"],"award-info":[{"award-number":["DBI-1707207"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P41GM103694"],"award-info":[{"award-number":["P41GM103694"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01GM125267"],"award-info":[{"award-number":["U01GM125267"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Glycan microarrays are capable of illuminating the interactions of glycan-binding proteins (GBPs) against hundreds of defined glycan structures, and have revolutionized the investigations of protein\u2013carbohydrate interactions underlying numerous critical biological activities. However, it is difficult to interpret microarray data and identify structural determinants promoting glycan binding to glycan-binding proteins due to the ambiguity in microarray fluorescence intensity and complexity in branched glycan structures. To facilitate analysis of glycan microarray data alongside protein structure, we have built the Glycan Microarray Database (GlyMDB), a web-based resource including a searchable database of glycan microarray samples and a toolset for data\/structure analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The current GlyMDB provides data visualization and glycan-binding motif discovery for 5203 glycan microarray samples collected from the Consortium for Functional Glycomics. The unique feature of GlyMDB is to link microarray data to PDB structures. The GlyMDB provides different options for database query, and allows users to upload their microarray data for analysis. After search or upload is complete, users can choose the criterion for binder versus non-binder classification. They can view the signal intensity graph including the binder\/non-binder threshold followed by a list of glycan-binding motifs. One can also compare the fluorescence intensity data from two different microarray samples. A protein sequence-based search is performed using BLAST to match microarray data with all available PDB structures containing glycans. The glycan ligand information is displayed, and links are provided for structural visualization and redirection to other modules in GlycanStructure.ORG for further investigation of glycan-binding sites and glycan structures.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/www.glycanstructure.org\/glymdb.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz934","type":"journal-article","created":{"date-parts":[[2019,12,11]],"date-time":"2019-12-11T20:11:21Z","timestamp":1576095081000},"page":"2438-2442","source":"Crossref","is-referenced-by-count":20,"title":["GlyMDB: Glycan Microarray Database and analysis toolset"],"prefix":"10.1093","volume":"36","author":[{"given":"Yiwei","family":"Cao","sequence":"first","affiliation":[{"name":"Departments of Biological Sciences and Bioengineering, Lehigh University , Bethlehem, PA 18015, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sang-Jun","family":"Park","sequence":"additional","affiliation":[{"name":"Departments of Biological Sciences and Bioengineering, Lehigh University , Bethlehem, PA 18015, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akul Y","family":"Mehta","sequence":"additional","affiliation":[{"name":"Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston , MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard D","family":"Cummings","sequence":"additional","affiliation":[{"name":"Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston , MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5642-6041","authenticated-orcid":false,"given":"Wonpil","family":"Im","sequence":"additional","affiliation":[{"name":"Departments of Biological Sciences and Bioengineering, Lehigh University , Bethlehem, PA 18015, USA"},{"name":"School of Computational Sciences, Korea Institute for Advanced Study , Seoul 02455, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,12,16]]},"reference":[{"key":"2023020108352088700_btz934-B1","doi-asserted-by":"crossref","first-page":"3417","DOI":"10.1093\/bioinformatics\/btu559","article-title":"GlycoPattern: a web platform for glycan array mining","volume":"30","author":"Agravat","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020108352088700_btz934-B2","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/S0304-4165(99)00165-8","article-title":"On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database","volume":"1473","author":"Apweiler","year":"1999","journal-title":"Biochim. Biophys. Acta"},{"key":"2023020108352088700_btz934-B3","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023020108352088700_btz934-B4","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1089\/omi.2012.0013","article-title":"Automated motif discovery from glycan array data","volume":"16","author":"Cholleti","year":"2012","journal-title":"OMICS"},{"key":"2023020108352088700_btz934-B5","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1023\/A:1012487302797","article-title":"Gene selection for cancer classification using support vector machines","volume":"46","author":"Guyon","year":"2002","journal-title":"Mach. Learn"},{"key":"2023020108352088700_btz934-B6","first-page":"10","article-title":"Preparation and analysis of glycan microarrays","volume":"12","author":"Heimburg-Molinaro","year":"2011","journal-title":"Curr. Protoc. Protein Sci"},{"key":"2023020108352088700_btz934-B7","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.carres.2018.05.003","article-title":"MCAW-DB: a glycan profile database capturing the ambiguity of glycan recognition patterns","volume":"464","author":"Hosoda","year":"2018","journal-title":"Carbohydr. Res"},{"key":"2023020108352088700_btz934-B8","doi-asserted-by":"crossref","first-page":"D470","DOI":"10.1093\/nar\/gks987","article-title":"Glycan fragment database: a database of PDB-based glycan 3D structures","volume":"41","author":"Jo","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023020108352088700_btz934-B9","doi-asserted-by":"crossref","first-page":"3135","DOI":"10.1002\/jcc.21886","article-title":"Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins","volume":"32","author":"Jo","year":"2011","journal-title":"J. Comput. Chem"},{"key":"2023020108352088700_btz934-B10","doi-asserted-by":"crossref","first-page":"W667","DOI":"10.1093\/nar\/gkq446","article-title":"GlycoViewer: a tool for visual summary and comparative analysis of the glycome","volume":"38","author":"Joshi","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023020108352088700_btz934-B11","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1007\/978-1-4939-2343-4_15","article-title":"Exploring the specificities of glycan-binding proteins using glycan array data and the GlycoSearch software","volume":"1273","author":"Kletter","year":"2015","journal-title":"Methods Mol. Biol"},{"key":"2023020108352088700_btz934-B12","doi-asserted-by":"crossref","first-page":"3536","DOI":"10.1093\/bioinformatics\/btz075","article-title":"GLAD: GLycan Array Dashboard, a visual analytics tool for glycan microarrays","volume":"35","author":"Mehta","year":"2019","journal-title":"Bioinformatics"},{"key":"2023020108352088700_btz934-B13","doi-asserted-by":"crossref","first-page":"3051","DOI":"10.1093\/bioinformatics\/btx358","article-title":"Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank","volume":"33","author":"Park","year":"2017","journal-title":"Bioinformatics"},{"key":"2023020108352088700_btz934-B14","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1146\/annurev-biochem-061809-152236","article-title":"Glycan microarrays for decoding the glycome","volume":"80","author":"Rillahan","year":"2011","journal-title":"Annu. Rev. Biochem"},{"key":"2023020108352088700_btz934-B15","doi-asserted-by":"crossref","first-page":"3755","DOI":"10.1093\/bioinformatics\/bty419","article-title":"NGL viewer: web-based molecular graphics for large complexes","volume":"34","author":"Rose","year":"2018","journal-title":"Bioinformatics"},{"key":"2023020108352088700_btz934-B16","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1038\/nmeth.4499","article-title":"LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data","volume":"14","author":"Sehnal","year":"2017","journal-title":"Nat. Methods"},{"key":"2023020108352088700_btz934-B17","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1093\/glycob\/cwx066","article-title":"GlyTouCan: an accessible glycan structure repository","volume":"27","author":"Tiemeyer","year":"2017","journal-title":"Glycobiology"},{"key":"2023020108352088700_btz934-B18","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1093\/glycob\/cww086","article-title":"Biological roles of glycans","volume":"27","author":"Varki","year":"2017","journal-title":"Glycobiology"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz934\/31836516\/btz934.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/8\/2438\/48983937\/bioinformatics_36_8_2438.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/8\/2438\/48983937\/bioinformatics_36_8_2438.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T19:47:24Z","timestamp":1675280844000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/8\/2438\/5678782"}},"subtitle":[],"editor":[{"given":"Arne","family":"Elofsson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,12,16]]},"references-count":18,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2020,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz934","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,4,15]]},"published":{"date-parts":[[2019,12,16]]}}}