BioReproducibility

While the ability to reproduce published results is generally recognized as a defining characteristic of science, in recent years there has been a growing realization many published biomedical research findings cannot be repeated outside of the laboratories that originally produced them.

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In the news:

•   75th Birthday of Alex Wlodawer
•   Brian Nosek, Center for Open Science: Open science is more important than ever

Selected papers addressing reproducibility issues

• Begley, C.G. and L.M. Ellis, Drug development: Raise standards for preclinical cancer research. Nature, 2012. 483(7391): 531-3.
• Prinz, F., T. Schlange, and K. Asadullah, Believe it or not: how much can we rely on published data on potential drug targets? Nat Rev Drug Discov, 2011. 10(9): 712.
• Carp, J., Better living through transparency: improving the reproducibility of fMRI results through comprehensive methods reporting. Cogn Affect Behav Neurosci, 2013. 13(3): 660-6.
• Collins, F.S. and L.A. Tabak, Policy: NIH plans to enhance reproducibility. Nature, 2014. 505(7485): 612-3. [PMCID:PMC4058759].
• McNutt, M., Raising the bar. Science, 2014. 345(6192): 9.
• Chruszcz, M., et al., Unmet challenges of structural genomics. Curr Opin Struct Biol, 2010. 20(5): 587-97. [PMCID:PMC3017768].
• Cheng, Q.D., et al. Effect of the weather conditions during solution preparation on lysozyme crystallization J. Appl. Cryst. (2017). 50, 1341-1351 link

Solutions

• The Center for Open Science. [cited 2014 October 9, 2014]; Available from: http://centerforopenscience.org.
• Majorek KA, Kuhn ML, Chruszcz M, Anderson WF, Minor W
  Double trouble-Buffer selection and His-tag presence may be responsible for nonreproducibility of biomedical experiments.
  Protein Sci. 2014. 23(10):1359-68. Times cited: 12. [Pub Med ID: 25044180] [Pub Med Central ID: PMC4286991]
• Zimmerman MD, Grabowski M, Domagalski MJ, Maclean EM, Chruszcz M, Minor W
  Data management in the modern structural biology and biomedical research environment.
  Methods Mol. Biol. 2014. 1140:1-25. Times cited: 6. [Pub Med ID: 24590705] [Pub Med Central ID: PMC4086192]
• Zheng H, Chruszcz M, Lasota P, Lebioda L, Minor W
  Data mining of metal ion environments present in protein structures.
  J. Inorg. Biochem. 2008. 102(9):1765-76. Times cited: 124. [Pub Med ID: 18614239] [Pub Med Central ID: PMC2872550

Tools to determine the quality of the structure and/or check if there is a potential purification artifact

• Covid-19.bioreproducibility.org Validated SARS-CoV-2 related structural models of potential drug targets
• HKL3000 - This program package allows for lattice parameter search against PDB [PMID: 16855301]
• molstack - This tool allows the visualization and analysis of multiple sets of coordinate and electron density data [PMID: 28815771]
• ContaMiner - This is a webserver for early identification of unwantedly crystallized protein contaminants by molecular replacement using structures of known artifacts [PMC5140001]
• SAUC - Search of Alternate Unit Cells - This server allows to search PDB for cells representing similar lattices