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Open AccessArticle
African Swine Fever Virus Protein–Protein Interaction Prediction
by
Jacob A. Fenster
Jacob A. Fenster 1,2,3,
Paul A. Azzinaro
Paul A. Azzinaro 2,3
,
Mark Dinhobl
Mark Dinhobl 2,3,
Manuel V. Borca
Manuel V. Borca 2,3,*,
Edward Spinard
Edward Spinard 2,3
and
Douglas P. Gladue
Douglas P. Gladue 2,3,*,†
1
Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
2
Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Orient, NY 11957, USA
3
National Bio and Agro-Defense Facility, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA
*
Authors to whom correspondence should be addressed.
†
Current address: Seek Labs, 350 W 800 N Suite 220, Salt Lake City, UT 84103, USA.
Viruses 2024, 16(7), 1170; https://doi.org/10.3390/v16071170 (registering DOI)
Submission received: 4 June 2024
/
Revised: 5 July 2024
/
Accepted: 12 July 2024
/
Published: 20 July 2024
Abstract
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–protein interactions between viral proteins and between viral and host proteins. In this work, we identified ASFV-ASFV protein–protein 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–protein interactions, further validating their relevance. Two protein–protein interactions, I267L and I8L, I267L__I8L, and B175L and DP79L, B175L__DP79L, are novel PPIs involving viral proteins known to modulate host immune response.
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MDPI and ACS Style
Fenster, J.A.; Azzinaro, P.A.; Dinhobl, M.; Borca, M.V.; Spinard, E.; Gladue, D.P.
African Swine Fever Virus Protein–Protein Interaction Prediction. Viruses 2024, 16, 1170.
https://doi.org/10.3390/v16071170
AMA Style
Fenster JA, Azzinaro PA, Dinhobl M, Borca MV, Spinard E, Gladue DP.
African Swine Fever Virus Protein–Protein Interaction Prediction. Viruses. 2024; 16(7):1170.
https://doi.org/10.3390/v16071170
Chicago/Turabian Style
Fenster, Jacob A., Paul A. Azzinaro, Mark Dinhobl, Manuel V. Borca, Edward Spinard, and Douglas P. Gladue.
2024. "African Swine Fever Virus Protein–Protein Interaction Prediction" Viruses 16, no. 7: 1170.
https://doi.org/10.3390/v16071170
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