{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T17:01:24Z","timestamp":1780765284139,"version":"3.54.1"},"reference-count":60,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,15]],"date-time":"2022-12-15T00:00:00Z","timestamp":1671062400000},"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\/501100010803","name":"Department of Biotechnology","doi-asserted-by":"publisher","award":["BT\/PR40158\/BTIS\/137\/24\/2021"],"award-info":[{"award-number":["BT\/PR40158\/BTIS\/137\/24\/2021"]}],"id":[{"id":"10.13039\/501100010803","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,19]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>There are a number of antigens that induce autoimmune response against \u03b2-cells, leading to type 1 diabetes mellitus (T1DM). Recently, several antigen-specific immunotherapies have been developed to treat T1DM. Thus, identification of T1DM associated peptides with antigenic regions or epitopes is important for peptide based-therapeutics (e.g. immunotherapeutic). In this study, for the first time, an attempt has been made to develop a method for predicting, designing, and scanning of T1DM associated peptides with high precision. We analysed 815 T1DM associated peptides and observed that these peptides are not associated with a specific class of HLA alleles. Thus, HLA binder prediction methods are not suitable for predicting T1DM associated peptides. First, we developed a similarity\/alignment based method using Basic Local Alignment Search Tool and achieved a high probability of correct hits with poor coverage. Second, we developed an alignment-free method using machine learning techniques and got a maximum AUROC of 0.89 using dipeptide composition. Finally, we developed a hybrid method that combines the strength of both alignment free and alignment-based methods and achieves maximum area under the receiver operating characteristic of 0.95 with Matthew\u2019s correlation coefficient of 0.81 on an independent dataset. We developed a web server \u2018DMPPred\u2019 and stand-alone server for predicting, designing and scanning T1DM associated peptides (https:\/\/webs.iiitd.edu.in\/raghava\/dmppred\/).<\/jats:p>","DOI":"10.1093\/bib\/bbac525","type":"journal-article","created":{"date-parts":[[2022,12,16]],"date-time":"2022-12-16T18:02:59Z","timestamp":1671213779000},"source":"Crossref","is-referenced-by-count":8,"title":["DMPPred: a tool for identification of antigenic regions responsible for inducing type 1 diabetes mellitus"],"prefix":"10.1093","volume":"24","author":[{"given":"Nishant","family":"Kumar","sequence":"first","affiliation":[{"name":"Indraprastha Institute of Information Technology Department of Computational Biology, , Okhla Phase 3, New Delhi-110020 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sumeet","family":"Patiyal","sequence":"additional","affiliation":[{"name":"Indraprastha Institute of Information Technology Department of Computational Biology, , Okhla Phase 3, New Delhi-110020 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shubham","family":"Choudhury","sequence":"additional","affiliation":[{"name":"Indraprastha Institute of Information Technology Department of Computational Biology, , Okhla Phase 3, New Delhi-110020 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ritu","family":"Tomer","sequence":"additional","affiliation":[{"name":"Indraprastha Institute of Information Technology Department of Computational Biology, , Okhla Phase 3, New Delhi-110020 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anjali","family":"Dhall","sequence":"additional","affiliation":[{"name":"Indraprastha Institute of Information Technology Department of Computational Biology, , Okhla Phase 3, New Delhi-110020 , India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8902-2876","authenticated-orcid":false,"given":"Gajendra P 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