{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T14:48:58Z","timestamp":1776091738404,"version":"3.50.1"},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2023,9,22]],"date-time":"2023-09-22T00:00:00Z","timestamp":1695340800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008921","name":"Saskatchewan Agriculture Development","doi-asserted-by":"crossref","award":["20210690"],"award-info":[{"award-number":["20210690"]}],"id":[{"id":"10.13039\/100008921","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,10,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Swine leukocyte antigens (SLAs) (i.e. swine major histocompatibility complex proteins) conduct a fundamental role in swine immunity. To generate a protective vaccine across an outbred species, such as pigs, it is critical that epitopes that bind to diverse SLA alleles are used in the vaccine development process. We introduced a new strategy for epitope prediction.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We employed molecular dynamics simulation to identify key amino acids for interactions with epitopes. We developed an algorithm wherein each SLA-1 is compared to a crystalized reference allele with unique weighting for non-conserved amino acids based on R group and position. We then performed homology modeling and electrostatic contact mapping to visualize how relatively small changes in sequences impacted the charge distribution in the binding site. We selected eight diverse SLA-1 alleles and performed homology modeling followed, by protein\u2013peptide docking and binding affinity analyses, to identify porcine reproductive and respiratory syndrome virus matrix protein epitopes that bind with high affinity to these alleles. We also performed docking analysis on the epitopes identified as strong binders using NetMHCpan 4.1. Epitopes predicted to bind to our eight SLA-1 alleles had equivalent or higher energetic interactions than those predicted to bind to the NetMHCpan 4.1 allele repertoire. This approach of selecting diverse SLA-1 alleles, followed by homology modeling, and docking simulations, can be used as a novel strategy for epitope prediction that complements other available tools and is especially useful when available tools do not offer a prediction for SLAs\/major histocompatibility complex.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The data underlying this article are available in the online Supplementary Material.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad590","type":"journal-article","created":{"date-parts":[[2023,9,23]],"date-time":"2023-09-23T04:04:12Z","timestamp":1695441852000},"source":"Crossref","is-referenced-by-count":4,"title":["Using a novel structure\/function approach to select diverse swine major histocompatibility complex 1 alleles to predict epitopes for vaccine development"],"prefix":"10.1093","volume":"39","author":[{"given":"Zahed","family":"Khatooni","sequence":"first","affiliation":[{"name":"Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan , Saskatoon, SK S7N 5E3, Canada"},{"name":"Department of Computer Science, University of Kurdistan , Sanandaj, Iran"}]},{"given":"Navid","family":"Teymourian","sequence":"additional","affiliation":[{"name":"Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan , Saskatoon, SK S7N 5B4, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1261-0901","authenticated-orcid":false,"given":"Heather L","family":"Wilson","sequence":"additional","affiliation":[{"name":"Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan , Saskatoon, SK S7N 5E3, Canada"},{"name":"Department of Computer Science, University of Kurdistan , Sanandaj, Iran"},{"name":"Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan , Saskatoon, SK S7N 5B4, Canada"},{"name":"Vaccinology & Immunotherapeutics Program, School of Public Health, University of Saskatchewan , Saskatoon, SK S7N 5B4, Canada"}]}],"member":"286","published-online":{"date-parts":[[2023,9,22]]},"reference":[{"key":"2023100505084833000_btad590-B1","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1-2","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"2023100505084833000_btad590-B2","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1093\/bioinformatics\/btv639","article-title":"Gapped sequence alignment using artificial neural 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