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As modulating \u22121 PRF can inhibit viral replication, the RNA pseudoknot stimulating \u22121 PRF may be a fruitful target for therapeutics treating COVID-19. We modeled the unusual 3-stem structure of the stimulatory pseudoknot of SARS-CoV-2 computationally, using multiple blind structural prediction tools followed by \u03bcs-long molecular dynamics simulations. The results were compared for consistency with nuclease-protection assays and single-molecule force spectroscopy measurements of the SARS-CoV-1 pseudoknot, to determine the most likely conformations. We found several possible conformations for the SARS-CoV-2 pseudoknot, all having an extended stem 3 but with different packing of stems 1 and 2. Several conformations featured rarely-seen threading of a single strand through junctions formed between two helices. These structural models may help interpret future experiments and support efforts to discover ligands inhibiting \u22121 PRF in SARS-CoV-2.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008603","type":"journal-article","created":{"date-parts":[[2021,1,19]],"date-time":"2021-01-19T13:45:19Z","timestamp":1611063919000},"page":"e1008603","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":40,"title":["Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0133-3531","authenticated-orcid":true,"given":"Sara Ibrahim","family":"Omar","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meng","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3581-8016","authenticated-orcid":true,"given":"Rohith Vedhthaanth","family":"Sekar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4781-6184","authenticated-orcid":true,"given":"Sahar Arbabi","family":"Moghadam","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9976-0429","authenticated-orcid":true,"given":"Jack A.","family":"Tuszynski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4695-0397","authenticated-orcid":true,"given":"Michael T.","family":"Woodside","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2021,1,19]]},"reference":[{"key":"pcbi.1008603.ref001","unstructured":"Coronavirus disease (COVID-19) Situation Report\u2014129. 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