{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T01:52:02Z","timestamp":1783475522242,"version":"3.55.0"},"reference-count":64,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2024,7,20]],"date-time":"2024-07-20T00:00:00Z","timestamp":1721433600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Oak Ridge Institute for Science and Education (ORISE)","award":["DE-SC0014664"],"award-info":[{"award-number":["DE-SC0014664"]}]},{"name":"U.S. Department of Energy (DOE)","award":["DE-SC0014664"],"award-info":[{"award-number":["DE-SC0014664"]}]},{"name":"U.S. Department of Agriculture (USDA)","award":["DE-SC0014664"],"award-info":[{"award-number":["DE-SC0014664"]}]},{"name":"ORAU","award":["DE-SC0014664"],"award-info":[{"award-number":["DE-SC0014664"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The African swine fever virus (ASFV) is an often deadly disease in swine and poses a threat to swine livestock and swine producers. With its complex genome containing more than 150 coding regions, developing effective vaccines for this virus remains a challenge due to a lack of basic knowledge about viral protein function and protein\u2013protein interactions between viral proteins and between viral and host proteins. In this work, we identified ASFV-ASFV protein\u2013protein interactions (PPIs) using artificial intelligence-powered protein structure prediction tools. We benchmarked our PPI identification workflow on the Vaccinia virus, a widely studied nucleocytoplasmic large DNA virus, and found that it could identify gold-standard PPIs that have been validated in vitro in a genome-wide computational screening. We applied this workflow to more than 18,000 pairwise combinations of ASFV proteins and were able to identify seventeen novel PPIs, many of which have corroborating experimental or bioinformatic evidence for their protein\u2013protein interactions, further validating their relevance. Two protein\u2013protein interactions, I267L and I8L, I267L__I8L, and B175L and DP79L, B175L__DP79L, are novel PPIs involving viral proteins known to modulate host immune response.<\/jats:p>","DOI":"10.3390\/v16071170","type":"journal-article","created":{"date-parts":[[2024,7,22]],"date-time":"2024-07-22T08:24:59Z","timestamp":1721636699000},"page":"1170","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["African Swine Fever Virus Protein\u2013Protein Interaction Prediction"],"prefix":"10.3390","volume":"16","author":[{"given":"Jacob A.","family":"Fenster","sequence":"first","affiliation":[{"name":"Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA"},{"name":"Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Orient, NY 11957, USA"},{"name":"National Bio and Agro-Defense Facility, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0172-6415","authenticated-orcid":false,"given":"Paul A.","family":"Azzinaro","sequence":"additional","affiliation":[{"name":"Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Orient, NY 11957, USA"},{"name":"National Bio and Agro-Defense Facility, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Dinhobl","sequence":"additional","affiliation":[{"name":"Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Orient, NY 11957, USA"},{"name":"National Bio and Agro-Defense Facility, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuel V.","family":"Borca","sequence":"additional","affiliation":[{"name":"Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Orient, NY 11957, USA"},{"name":"National Bio and Agro-Defense Facility, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7268-6580","authenticated-orcid":false,"given":"Edward","family":"Spinard","sequence":"additional","affiliation":[{"name":"Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Orient, NY 11957, USA"},{"name":"National Bio and Agro-Defense Facility, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Douglas P.","family":"Gladue","sequence":"additional","affiliation":[{"name":"Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Orient, NY 11957, USA"},{"name":"National Bio and Agro-Defense Facility, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,7,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1016\/j.str.2022.02.004","article-title":"Exploring protein-protein interactions at the proteome level","volume":"30","author":"Elhabashy","year":"2022","journal-title":"Structure"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1016\/j.tibs.2023.03.003","article-title":"Recent advances in predicting and modeling protein\u2013protein interactions","volume":"48","author":"Durham","year":"2023","journal-title":"Trends Biochem. 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