{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T12:32:29Z","timestamp":1791549149752,"version":"4.3.4"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: N-linked glycosylation occurs predominantly at the N-X-T\/S motif, where X is any amino acid except proline. Not all N-X-T\/S sequons are glycosylated, and a number of web servers for predicting N-linked glycan occupancy using sequence and\/or residue pattern information have been developed. None of the currently available servers, however, utilizes protein structural information for the prediction of N-glycan occupancy.<\/jats:p><jats:p>Results: Here, we describe a novel classifier algorithm, NGlycPred, for the prediction of glycan occupancy at the N-X-T\/S sequons. The algorithm utilizes both structural as well as residue pattern information and was trained on a set of glycosylated protein structures using the Random Forest algorithm. The best predictor achieved a balanced accuracy of 0.687 under 10-fold cross-validation on a curated dataset of 479 N-X-T\/S sequons and outperformed sequence-based predictors when evaluated on the same dataset. The incorporation of structural information, including local contact order, surface accessibility\/composition and secondary structure thus improves the prediction accuracy of glycan occupancy at the N-X-T\/S consensus sequon.<\/jats:p><jats:p>Availability and Implementation: NGlycPred is freely available to non-commercial users as a web-based server at http:\/\/exon.niaid.nih.gov\/nglycpred\/.<\/jats:p><jats:p>Contact: \u00a0ivelin.georgiev@nih.gov<\/jats:p><jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts426","type":"journal-article","created":{"date-parts":[[2012,7,11]],"date-time":"2012-07-11T02:46:38Z","timestamp":1341974798000},"page":"2249-2255","source":"Crossref","is-referenced-by-count":86,"title":["Computational prediction of N-linked glycosylation incorporating structural properties and patterns"],"prefix":"10.1093","volume":"28","author":[{"given":"Gwo-Yu","family":"Chuang","sequence":"first","affiliation":[{"name":"Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey C.","family":"Boyington","sequence":"additional","affiliation":[{"name":"Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. 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