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

doi:10.1107/S2052252521003018

Rapid response to emerging biomedical challenges and threats

IUCrJ. 2021 Mar 26;8(Pt 3):395-407. doi: 10.1107/S2052252521003018. eCollection 2021 May 1.

Authors

Marek Grabowski¹, Joanna M Macnar^{1

2

3}, Marcin Cymborowski¹, David R Cooper¹, Ivan G Shabalin¹, Miroslaw Gilski^{4

5}, Dariusz Brzezinski^{1

5

6}, Marcin Kowiel⁵, Zbigniew Dauter⁷, Bernhard Rupp^{8

9}, Alexander Wlodawer⁷, Mariusz Jaskolski^{4

5}, Wladek Minor¹

Affiliations

¹ Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA.
² College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland.
³ Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Warsaw, Poland.
⁴ Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.
⁵ Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
⁶ Institute of Computing Science, Poznan University of Technology, Poznan, Poland.
⁷ Center for Structural Biology, National Cancer Institute, Frederick, Maryland, USA.
⁸ k.-k Hofkristallamt, San Diego, California, USA.
⁹ Institute of Genetic Epidemiology, Medical University Innsbruck, Innsbruck, Austria.

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.

Keywords: COVID-19; SARS-COV-2; bioreproducibility; coronavirus; information noise; pandemic.

Grants and funding

R01 GM132595/GM/NIGMS NIH HHS/United States