{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:04Z","timestamp":1753875784459,"version":"3.41.2"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2021,5,13]],"date-time":"2021-05-13T00:00:00Z","timestamp":1620864000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Fundacion Instituto de Inmunologia de Colombia"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Experimentally estimating peptide\u2013major histocompatibility complex (pMHC) binding affinity has been quite challenging due to the many receptors and the many potential ligands implicated in it. We have thus proposed a straightforward computational methodology considering the different mechanisms involved in pMHC binding to facilitate studying such receptor\u2013ligand interactions. We have developed a pipeline using semi-empirical quantum mechanical methods for calculating pMHC class I and II molecules\u2019 binding energy (BE). This pipeline can systematize the methodology for calculating pMHC system BE, enabling the rational design of T-cell epitopes to be used as pharmaceuticals and vaccines.<\/jats:p>","DOI":"10.1093\/bib\/bbab171","type":"journal-article","created":{"date-parts":[[2021,4,12]],"date-time":"2021-04-12T19:22:00Z","timestamp":1618255320000},"source":"Crossref","is-referenced-by-count":2,"title":["MHCBI: a pipeline for calculating peptide-MHC binding energy using semi-empirical quantum mechanical methods with explicit\/implicit solvent models"],"prefix":"10.1093","volume":"22","author":[{"given":"Carlos A","family":"Ortiz-Mahecha","sequence":"first","affiliation":[{"name":"Fundaci\u00f3n Instituto de Inmunolog\u00eda de Colombia, Bogota DC, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William A","family":"Agudelo","sequence":"additional","affiliation":[{"name":"Fundaci\u00f3n Instituto de Inmunolog\u00eda de Colombia, Bogota DC, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manuel A","family":"Patarroyo","sequence":"additional","affiliation":[{"name":"Fundaci\u00f3n Instituto de Inmunolog\u00eda de Colombia, Bogota DC, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manuel E","family":"Patarroyo","sequence":"additional","affiliation":[{"name":"Fundaci\u00f3n Instituto de Inmunolog\u00eda de Colombia, Bogota DC, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlos F","family":"Su\u00e1rez","sequence":"additional","affiliation":[{"name":"Fundaci\u00f3n Instituto de Inmunolog\u00eda de Colombia, Bogota DC, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,5,13]]},"reference":[{"key":"2021110814400718300_ref1","doi-asserted-by":"crossref","first-page":"292","DOI":"10.3389\/fimmu.2017.00292","article-title":"Major histocompatibility complex (MHC) class I and MHC class II proteins: conformational plasticity in antigen presentation","volume":"8","author":"Wieczorek","year":"2017","journal-title":"Front Immunol"},{"issue":"11","key":"2021110814400718300_ref2","doi-asserted-by":"crossref","first-page":"724","DOI":"10.1016\/j.it.2016.08.010","article-title":"Present yourself! 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