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Bijak V, Gucwa M, Lenkiewicz J, Murzyn K, Cooper DR, Minor W. Continuous Validation Across Macromolecular Structure Determination Process. NIHON KESSHO GAKKAI SHI 2023; 65:10-16. [PMID: 37416056 PMCID: PMC10321142 DOI: 10.5940/jcrsj.65.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The overall quality of the experimentally determined structures contained in the PDB is exceptionally high, mainly due to the continuous improvement of model building and structural validation programs. Improving reproducibility on a large scale requires expanding the concept of validation in structural biology and all other disciplines to include a broader framework that encompasses the entire project. A successful approach to science requires diligent attention to detail and a focus on the future. An earnest commitment to data availability and reuse is essential for scientific progress, be that by human minds or artificial intelligence.
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Affiliation(s)
- Vanessa Bijak
- Department of Molecular Physiology and Biological Physics, University of Virginia
| | - Michal Gucwa
- Department of Molecular Physiology and Biological Physics, University of Virginia
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University
| | - Joanna Lenkiewicz
- Department of Molecular Physiology and Biological Physics, University of Virginia
| | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University
| | - David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia
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Zhang H, Chen P, Ma H, Woińska M, Liu D, Cooper DR, Peng G, Peng Y, Deng L, Minor W, Zheng H. virusMED: an atlas of hotspots of viral proteins. IUCRJ 2021; 8:S2052252521009076. [PMID: 34614039 PMCID: PMC8479994 DOI: 10.1107/s2052252521009076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Metal binding sites, antigen epitopes and drug binding sites are the hotspots in viral proteins that control how viruses interact with their hosts. virusMED (virus Metal binding sites, Epitopes and Drug binding sites) is a rich internet application based on a database of atomic interactions around hotspots in 7041 experimentally determined viral protein structures. 25306 hotspots from 805 virus strains from 75 virus families were characterized, including influenza, HIV-1 and SARS-CoV-2 viruses. Just as Google Maps organizes and annotates points of interest, virusMED presents the positions of individual hotspots on each viral protein and creates an atlas upon which newly characterized functional sites can be placed as they are being discovered. virusMED contains an extensive set of annotation tags about the virus species and strains, viral hosts, viral proteins, metal ions, specific antibodies and FDA-approved drugs, which permits rapid screening of hotspots on viral proteins tailored to a particular research problem. The virusMED portal (https://virusmed.biocloud.top) can serve as a window to a valuable resource for many areas of virus research and play a critical role in the rational design of new preventative and therapeutic agents targeting viral infections.
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Affiliation(s)
- HuiHui Zhang
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
| | - Pei Chen
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
| | - Haojie Ma
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
| | - Magdalena Woińska
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
- University of Virginia, Charlottesville, VA 22908, USA
| | - Dejian Liu
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
| | | | - Guo Peng
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
| | - Yousong Peng
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
| | - Lei Deng
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
- Hunan Provincial Key Laboratory of Medical Virology, People’s Republic of China
| | - Wladek Minor
- University of Virginia, Charlottesville, VA 22908, USA
| | - Heping Zheng
- Hunan University College of Biology, Bioinformatics Center, Hunan 410082, People’s Republic of China
- Hunan Provincial Key Laboratory of Medical Virology, People’s Republic of China
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Grabowski M, Macnar JM, Cymborowski M, Cooper DR, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Dauter Z, Rupp B, Wlodawer A, Jaskolski M, Minor W. Rapid response to emerging biomedical challenges and threats. IUCRJ 2021; 8:395-407. [PMID: 33953926 PMCID: PMC8086160 DOI: 10.1107/s2052252521003018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/22/2021] [Indexed: 05/13/2023]
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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Affiliation(s)
- Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Joanna M. Macnar
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Warsaw, Poland
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Miroslaw Gilski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Marcin Kowiel
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Zbigniew Dauter
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland, USA
| | - Bernhard Rupp
- k.-k Hofkristallamt, San Diego, California, USA
- Institute of Genetic Epidemiology, Medical University Innsbruck, Innsbruck, Austria
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland, USA
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
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