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SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome
Maxwell I. Zimmerman, Justin R. Porter, Michael D. Ward and 15 more
Nature Chemistry · 2021
doi:10.1038/s41557-021-00707-0
References 74
- 1.
- 2.
Liu Y, Gayle AA, Wilder-Smith A & Rocklöv J The reproductive number of COVID-19 is higher compared to SARS coronavirus. J Travel Med 27, (2020 ).
Not in our library10.1093/jtm/taaa021
- 3.
Sorci G, Faivre B & Morand S Why Does COVID-19 Case Fatality Rate Vary Among Countries? SSRN Journal (2020 )
Not in our library10.2139/ssrn.3576892
- 4.
Morteza Abdullatif Khafaie FR Cross-Country Comparison of Case Fatality Rates of COVID-19/SARS-COV-2. Osong Public Health and Research Perspectives 11, 74–80 (2020 ).
Not in our library10.24171/j.phrp.2020.11.2.03
- 5.
Mahase E Coronavirus: covid-19 has killed more people than SARS and MERS combined, despite lower case fatality rate. BMJ 368, m641 (2020 ).
Not in our library10.1136/bmj.m641
- 6.
Onder G, Rezza G & Brusaferro S Case-Fatality Rate and Characteristics of Patients Dying in Relation to COVID-19 in Italy. JAMA 323, 1775–1776 (2020 ).
Not in our library10.1001/jama.2020.4683
- 7.
- 8.
Voelz VA, Bowman GR, Beauchamp K & Pande VS Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1–39). J. Am. Chem. Soc 132, 1526–1528 (2010 ).
Not in our library10.1021/ja9090353
- 9.
Lindorff-Larsen K, Piana S, Dror RO & Shaw DE How Fast-Folding Proteins Fold. Science 334, 517–520 (2011 ).
Not in our library10.1126/science.1208351
- 10.
Stodden V Enabling Reproducible Research: Open Licensing for Scientific Innovation. (2009 ).
Not in our library
- 11.
Amaro RE & Mulholland AJ A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19. Journal of Chemical Information and Modeling 60, 2653–2656 (2020 ).
Not in our library10.1021/acs.jcim.0c00319
- 12.
Shirts M & Pande VS COMPUTING: Screen Savers of the World Unite! Science 290, 1903–1904 (2000 ).
Not in our library10.1126/science.290.5498.1903
- 13.
Kohlhoff KJ Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. Nature Chem 6, 15–21 (2014 ).
Not in our library10.1038/nchem.1821
- 14.
Shukla D, Meng Y, Roux B & Pande VS Activation pathway of Src kinase reveals intermediate states as targets for drug design. Nat Commun 5, 1–11 (2014 ).
Not in our library10.1038/ncomms4397
- 15.
Sun X, Singh S, Blumer KJ & Bowman GR Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding. eLife 7, 19 (2018 ).
Not in our library10.7554/elife.38465
- 16.
- 17.
Chen S The dynamic conformational landscape of the protein methyltransferase SETD8. eLife 8, 213 (2019 ).
Not in our library10.7554/elife.45403
- 18.
Porter JR, Meller A, Zimmerman MI, Greenberg MJ & Bowman GR Conformational distributions of isolated myosin motor domains encode their mechanochemical properties. eLife 9, 19 (2020 ).
Not in our library10.7554/elife.55132
- 19.
Hart KM Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators. PLOS ONE 12, e0178678 (2017 ).
Not in our library10.1371/journal.pone.0178678
- 20.
Cruz MA Discovery of a cryptic allosteric site in Ebola’s ‘undruggable’ VP35 protein using simulations and experiments. bioRxiv 17, 2020.02.09.940510 (2020 ).
Not in our library
- 21.
- 22.
- 23.
Walls AC Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell 181, 281–292.e6 (2020 ).
Not in our library10.1016/j.cell.2020.02.058
- 24.
Wrapp D Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 367, 1260–1263 (2020 ).
Not in our library10.1126/science.abb2507
- 25.
Zhang H, Penninger JM, Li Y, Zhong N & Slutsky AS Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target. Intensive Care Med 46, 586–590 (2020 ).
Not in our library10.1007/s00134-020-05985-9
- 26.
Hoffmann M SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell 181, 271–280.e8 (2020 ).
Not in our library10.1016/j.cell.2020.02.052
- 27.
- 28.
Casalino L Shielding and Beyond: The Roles of Glycans in SARS-CoV-2 Spike Protein. 9, 221–27 (2020 ).
Not in our library10.1021/acscentsci.0c01056
- 29.
Zimmerman MI & Bowman GR FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs. J. Chem. Theory Comput 11, 5747–5757 (2015 ).
Not in our library10.1021/acs.jctc.5b00737
- 30.
Zimmerman MI & Bowman GR How to Run FAST Simulations. Methods in Enzymology 578, 213–225 (2016 ).
Not in our library10.1016/bs.mie.2016.05.032
- 31.
Sikora M Map of SARS-CoV-2 spike epitopes not shielded by glycans. bioRxiv 2020.07.03.186825 (2020 )
Not in our library10.1101/2020.07.03.186825
- 32.
- 33.
- 34.
Zhou T A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike. bioRxiv 16, 2020.07.04.187989 (2020 ).
Not in our library
- 35.
Guo L Engineered Trimeric ACE2 Binds and Locks ‘Three-up’ Spike Protein to Potently Inhibit SARS-CoVs and Mutants. bioRxiv 2020.08.31.274704 (2020 )
Not in our library10.1101/2020.08.31.274704
- 36.
Barnes CO Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies. bioRxiv 584, 2020.08.30.273920 (2020 ).
Not in our library
- 37.
Huo J Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike. SSRN Journal (2020 )
Not in our library10.2139/ssrn.3613273
- 38.
Zhong NS Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People’s Republic of China, in February, 2003. The Lancet 362, 1353–1358 (2003 ).
Not in our library10.1016/s0140-6736(03)14630-2
- 39.
van der Hoek L Identification of a new human coronavirus. Nat Med 10, 368–373 (2004 ).
Not in our library10.1038/nm1024
- 40.
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