journal article·2021-05-01Open access

Rapid response to emerging biomedical challenges and threats

Marek Grabowski, Joanna M. Macnar, Marcin Cymborowski, David R. Cooper, Ivan G. Shabalin, Miroslaw Gilski, Dariusz Brzezinski, Marcin Kowiel, Zbigniew Dauter, Bernhard Rupp, Alexander Wlodawer, Mariusz Jaskolski, Wladek Minor

IUCrJ· Volume 8· Issue 3

Abstract

As part of the global mobilization to combat the present pandemic, almost 100 000 COVID-19-related papers have been published and nearly a thousand models of macromolecules encoded by SARS-CoV-2 have been deposited in the Protein Data Bank within less than a year. The avalanche of new structural data has given rise to multiple resources dedicated to assessing the correctness and quality of structural data and models. Here, an approach to evaluate the massive amounts of such data using the resource https://covid19.bioreproducibility.org is described, which offers a template that could be used in large-scale initiatives undertaken in response to future biomedical crises. Broader use of the described methodology could considerably curtail information noise and significantly improve the reproducibility of biomedical research.
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Research context

OpenAlex topics: Enzyme Structure and Function · Advanced Proteomics Techniques and Applications · Protein Structure and Dynamics

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

References (58)

Show source-provided references
1. Báez-Santos · Antiviral Res. · 2015 · 115 · 2110.1016/j.antiviral.2014.12.015 ↗
2. Berman · Nucleic Acids Res. · 2000 · 28 · 23510.1093/nar/28.1.235 ↗
3. Berman · Nucleic Acids Res. · 2009 · 37 · D36510.1093/nar/gkn790 ↗
4. Brzezinski · FEBS J. · 2020 · 287 · 268510.1111/febs.15314 ↗
5. Brzezinski · Protein Sci. · 2021 · 30 · 11510.1002/pro.3959 ↗
6. Burley · Nucleic Acids Res. · 2019 · 47 · D46410.1093/nar/gky1004 ↗
7. Chen · Hum. Vaccin. Immunother. · 2014 · 10 · 64810.4161/hv.27464 ↗
8. Chou · Acta Cryst. D · 2014 · 70 · 57210.1107/S1399004713031040 ↗
9. Chruszcz · Curr. Opin. Struct. Biol. · 2010 · 20 · 58710.1016/j.sbi.2010.08.001 ↗
10. Clegg · IUCrJ · 2021 · 8 · 410.1107/S205225252001458X ↗
11. Cooper · Methods Mol. Biol. · 2021 · 2199 · 20910.1007/978-1-0716-0892-0_13 ↗
12. Croll · bioRxiv · 2020 · 20201007307546
13. Croll · Biophys. J. · 2021 · 120 · 108510.1016/j.bpj.2020.12.029 ↗
14. Ewers · J. Clin. Epidemiol. · 2021 · 130 · 14310.1016/j.jclinepi.2020.10.008 ↗
15. Faezov · bioRxiv · 2021 · 20210214431128
16. Grabowski · Struct. Dyn. · 2019 · 6 · 06430110.1063/1.5128672 ↗
17. Grabowski · Acta Cryst. D · 2016 · 72 · 118110.1107/S2059798316014716 ↗
18. Grabowski · J. Struct. Funct. Genomics · 2016 · 17 · 110.1007/s10969-016-9201-5 ↗
19. Hall-Swan · bioRxiv · 2021 · 20210121427315
20. Helliwell · IUCrJ · 2019 · 6 · 34110.1107/S2052252519005918 ↗
21. Henderson · J. Chem. Phys. · 2020 · 153 · 11510110.1063/5.0020458 ↗
22. Iudin · Nat. Methods · 2016 · 13 · 38710.1038/nmeth.3806 ↗
23. Jaskolski · Methods Mol. Biol. · 2017 · 1607 · 54910.1007/978-1-4939-7000-1_22 ↗
24. Jaskolski · Acta Cryst. D · 2007 · 63 · 61110.1107/S090744490700978X ↗
25. Kabsch · Acta Cryst. D · 2010 · 66 · 12510.1107/S0907444909047337 ↗
26. Kolesov · Nucleic Acids Res. · 2007 · 35 · W42510.1093/nar/gkm312 ↗
27. Kowiel · Bioinformatics · 2019 · 35 · 45210.1093/bioinformatics/bty626 ↗
28. Lei · Antiviral Res. · 2018 · 149 · 5810.1016/j.antiviral.2017.11.001 ↗
29. Leslie · Acta Cryst. D · 2006 · 62 · 4810.1107/S0907444905039107 ↗
30. Liebschner · Acta Cryst. D · 2021 · 77 · 4810.1107/S2059798320015879 ↗
31. Lubin · bioRxiv · 2020 · 20201201406637
32. Macnar · Biomolecules · 2020 · 10 · 46110.3390/biom10030461 ↗
33. Masmaliyeva · Acta Cryst. D · 2019 · 75 · 50510.1107/S2059798319004807 ↗
34. McPherson · Nat. Methods · 2009 · 6 · S210.1038/nmeth.f.268 ↗
35. Meyer · Nat. Commun. · 2016 · 7 · 1088210.1038/ncomms10882 ↗
36. Minor · Acta Cryst. D · 2006 · 62 · 85910.1107/S0907444906019949 ↗
37. Minor · Structure · 2016 · 24 · 21610.1016/j.str.2015.12.010 ↗
38. Miyakawa · Mol. Brain · 2020 · 13 · 2410.1186/s13041-020-0552-2 ↗
39. Osipiuk · Nat. Commun. · 2021 · 12 · 74310.1038/s41467-021-21060-3 ↗
40. Otwinowski · Methods Enzymol. · 1997 · 276 · 30710.1016/S0076-6879(97)76066-X ↗
41. Parks · N. Engl. J. Med. · 2020 · 382 · 226110.1056/NEJMcibr2007042 ↗
42. Pearce · Acta Cryst. D · 2017 · 73 · 25610.1107/S2059798317003412 ↗
43. Raczynska · Drug Resist. Updat. · 2018 · 40 · 110.1016/j.drup.2018.08.001 ↗
44. Rahman · J. Tradit. Complement. Med. · 2021 · 11 · 17310.1016/j.jtcme.2021.01.006 ↗
45. Rupp, B. (2009). Biomolecular Crystallography: Principles, Practice, and Application to Structural Biology. New York: Garland Science.10.1201/9780429258756 ↗
46. Sedova · Bioinformatics · 2020 · 36 · 436010.1093/bioinformatics/btaa550 ↗
47. Shabalin · Acta Cryst. D · 2015 · 71 · 196510.1107/S139900471500629X ↗
48. Singh · J. Pharmacol. Pharmacother. · 2011 · 2 · 13810.4103/0976-500X.81919 ↗
49. Touw · J. Mol. Biol. · 2016 · 428 · 137510.1016/j.jmb.2016.02.002 ↗
50. Waman, V. P., Sen, N., Varadi, M., Daina, A., Wodak, S. J., Zoete, V., Velankar, S. & Orengo, C. (2020). Brief. Bioinform., bbaa362.
51. Ward · J. Am. Stat. Assoc. · 1963 · 58 · 23610.1080/01621459.1963.10500845 ↗
52. Winter · Acta Cryst. D · 2018 · 74 · 8510.1107/S2059798317017235 ↗
53. Wlodawer · FEBS J. · 2018 · 285 · 44410.1111/febs.14320 ↗
54. Wlodawer · FEBS J. · 2020 · 287 · 370310.1111/febs.15366 ↗
55. Wlodawer · FEBS J. · 2013 · 280 · 570510.1111/febs.12495 ↗
56. Zheng · Exp. Opin. Drug. Discov. · 2014 · 9 · 12510.1517/17460441.2014.872623 ↗
57. Zheng · Methods Mol. Biol. · 2017 · 1607 · 64310.1007/978-1-4939-7000-1_27 ↗
58. Zimmerman · Methods Mol. Biol. · 2014 · 1140 · 110.1007/978-1-4939-0354-2_1 ↗