SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome

References 74

1. 1.
   A pneumonia outbreak associated with a new coronavirus of probable bat origin · 2020

   No notice
2. 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. 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. 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. 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. 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. 7.
   Molecular Docking and Structure-Based Drug Design Strategies · 2015

   No notice
8. 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. 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. 10.

    Stodden V Enabling Reproducible Research: Open Licensing for Scientific Innovation. (2009 ).

    Not in our library

11. 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. 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. 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. 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. 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. 16.
    Modelling proteins’ hidden conformations to predict antibiotic resistance · 2016

    No notice
17. 17.

    Chen S The dynamic conformational landscape of the protein methyltransferase SETD8. eLife 8, 213 (2019 ).

    Not in our library10.7554/elife.45403

18. 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. 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. 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. 21.
    The Cap-Snatching SFTSV Endonuclease Domain Is an Antiviral Target · 2020

    Not checked
22. 22.
    Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis · 2018

    Corrected
23. 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. 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. 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. 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. 27.
    Vulnerabilities in coronavirus glycan shields despite extensive glycosylation · 2020

    No notice
28. 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. 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. 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. 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. 32.
    In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges · 2020

    No notice
33. 33.
    Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains · 2017

    No notice
34. 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. 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. 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. 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. 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. 39.

    van der Hoek L Identification of a new human coronavirus. Nat Med 10, 368–373 (2004 ).

    Not in our library10.1038/nm1024

40. 40.
    Cell entry mechanisms of SARS-CoV-2 · 2020

    No notice
41. 41.

    Wu K, Li W, Peng G & Li F Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor. PNAS 106, 19970–19974 (2009 ).

    Not in our library10.1073/pnas.0908837106

42. 42.

    Shang J Structural basis of receptor recognition by SARS-CoV-2. Nature 581, 221–224 (2020 ).

    Not in our library10.1038/s41586-020-2179-y

43. 43.

    Graham BS, Gilman MSA & McLellan JS Structure-Based Vaccine Antigen Design. Annu. Rev. Med 70, 91–104 (2019 ).

    Not in our library10.1146/annurev-med-121217-094234

44. 44.
    Linear epitopes of SARS-CoV-2 spike protein elicit neutralizing antibodies in COVID-19 patients · 2020

    No notice
45. 45.
    Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability · 2020

    No notice
46. 46.
    Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail · 2020

    No notice
47. 47.
    Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors · 2020

    No notice
48. 48.

    Graziano Vito, McGrath William J, Yang Lin, Walter A, Mangel F. SARS CoV Main Proteinase: The Monomer–Dimer Equilibrium Dissociation Constant. Biochemistry 45, 14632–14641 (American Chemical Society, 2006 ).

    Not in our library10.1021/bi061746y

49. 49.

    Goyal B & Goyal D Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy. ACS Combinatorial Science 22, 297–305 (2020 ).

    Not in our library10.1021/acscombsci.0c00058

50. 50.

    Porter JR Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric Coupling. Biophysical Journal 116, 818–830 (2019 ).

    Not in our library10.1016/j.bpj.2018.11.3144

51. 51.
    The Coronavirus Nucleocapsid Is a Multifunctional Protein · 2014

    No notice
52. 52.

    Masters PS Coronavirus genomic RNA packaging. Virology 537, 198–207 (2019 ).

    Not in our library10.1016/j.virol.2019.08.031

53. 53.
    The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA · 2021

    No notice
54. 54.

    Su Z Electron Cryo-microscopy Structure of Ebola Virus Nucleoprotein Reveals a Mechanism for Nucleocapsid-like Assembly. Cell 172, 966–978.e12 (2018 ).

    Not in our library10.1016/j.cell.2018.02.009

55. 55.
    Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein · 2020

    No notice
56. 56.
    SWISS-MODEL: homology modelling of protein structures and complexes · 2018

    No notice
57. 57.

    Jo S, Kim T, Iyer VG & Im W CHARMM-GUI: a web-based graphical user interface for CHARMM. Journal of computational chemistry 29, 1859–1865 (2008 ).

    Not in our library10.1002/jcc.20945

58. 58.

    Lee J CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. J. Chem. Theory Comput 12, 405–413 (2016 ).

    Not in our library10.1021/acs.jctc.5b00935

59. 59.

    Chodera J, Lee AA, London N & Delft von, F. Crowdsourcing drug discovery for pandemics. Nature Chem 12, 581–581 (2020 ).

    Not in our library10.1038/s41557-020-0496-2

60. 60.

    Abraham MJ GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015 ).

    Not in our library

61. 61.

    Duan Y A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24, 1999–2012 (2003 ).

    Not in our library10.1002/jcc.10349

62. 62.

    Huang J & MacKerell AD CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J Comput Chem 34, 2135–2145 (2013 ).

    Not in our library10.1002/jcc.23354

63. 63.

    Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW & Klein ML Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics 79, 926–935 (1983 ).

    Not in our library

64. 64.

    Hess B P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation. J. Chem. Theory Comput 4, 116–122 (2008 ).

    Not in our library10.1021/ct700200b

65. 65.

    Bussi G, Donadio D & Parrinello M Canonical sampling through velocity rescaling. The Journal of Chemical Physics 126, 014101 (2007 ).

    Not in our library10.1063/1.2408420

66. 66.

    Zimmerman MI Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models. ACS Cent Sci 3, 1311–1321 (2017 ).

    Not in our library10.1021/acscentsci.7b00465

67. 67.

    Hendlich M, Rippmann F & Barnickel G LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graph. Model 15, 359–63–389 (1997 ).

    Not in our library10.1016/s1093-3263(98)00002-3

68. 68.
    OpenMM 7: Rapid development of high performance algorithms for molecular dynamics · 2017

    No notice
69. 69.

    Husic BE & Pande VS Markov State Models: From an Art to a Science. J. Am. Chem. Soc 140, 2386–2396 (2018 ).

    Not in our library10.1021/jacs.7b12191

70. 70.

    Porter JR, Zimmerman MI & Bowman GR Enspara: Modeling molecular ensembles with scalable data structures and parallel computing. The Journal of Chemical Physics 150, 044108 (2019 ).

    Not in our library10.1063/1.5063794

71. 71.

    Zimmerman MI, Porter JR, Sun X, Silva RR & Bowman GR Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes. J. Chem. Theory Comput 14, 5459–5475 (2018 ).

    Not in our library10.1021/acs.jctc.8b00500

72. 72.

    McGibbon RT MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. Biophysical Journal 109, 1528–1532 (2015 ).

    Not in our library10.1016/j.bpj.2015.08.015

73. 73.
    UniProt: a worldwide hub of protein knowledge · 2018

    No notice
74. 74.

    Edgar RC MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004 ).

    Not in our library10.1093/nar/gkh340

Cited by papers we hold 3

• Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network · 2023
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• Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors · 2023
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• Computational epitope map of SARS-CoV-2 spike protein · 2021
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