Safeguarding Structural Data Repositories against Bad Apples

Minor, Władek; Dauter, Zbigniew; Helliwell, John R.; Jaskólski, Mariusz; Wlodawer, Alexander

doi:10.1016/j.str.2015.12.010

Cited by 37 publications

(56 citation statements)

References 25 publications

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“…The field of Zn coordination by macromolecules is sufficiently well grounded on the previous, competent studies, such as those presented in Refs. As another conclusion we reiterate the opinion that the field of structural biology should continue to be on the lookout and safeguard itself against fallacious data‐mining meta‐analyses, as well as against individual bad apples (macromolecular structures, especially with small‐molecule components) that contaminate our repositories …”

Section: Discussionmentioning

confidence: 71%

“…In order to perform a meaningful meta‐analysis, it is essential to ensure proper quality control of the input data. It has been pointed out more than once that one bad apple can spoil a whole bushel of decent data points . All that the authors seem to have done in this respect was to limit the resolution of the input structures to better than 3 Å, and examine the B factors of the ligands involved in unusual angles and to compare them to the average B factor for all the ligands.…”

Section: Discussionmentioning

confidence: 99%

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Prior knowledge or freedom of interpretation? A critical look at a recently published classification of “novel” Zn binding sites

2016

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In a recently published paper [Yao, S., Flight, R.M., Rouchka, E.C. & Moseley, H.N. (2015). Proteins 83, 1470–1487] the authors propose novel Zn coordination patterns in protein structures, apparently discovered using an unprejudiced approach to the information collected in the Protein data Bank (PDB), which they advocate as superior to the prior-knowledge-informed paradigm. In our assessment of those propositions we demonstrate here that most, if not all, of the ‘new’ coordination geometries are fictitious, as they are based on incorrectly interpreted protein crystal structures, which in themselves are often not error-free. The flaws of interpretation include partial or wrong Zn sites, missed or wrong ligands, ignored crystal symmetry and ligands, etc. In conclusion, we warn against using this and similar meta-analyses that ignore chemical and crystallographic knowledge, and emphasize the importance of safeguarding structural databases against bad apples.

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Section: Discussionmentioning

confidence: 71%

Section: Discussionmentioning

confidence: 99%

Prior knowledge or freedom of interpretation? A critical look at a recently published classification of “novel” Zn binding sites

2016

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“…The importance of retaining raw diffraction data has been emphasized numerous times (Jones et al, 1996;Androulakis et al, 2008;Baker et al, 2008;Jovine et al, 2008;Rupp, 2012;Domagalski et al, 2014;Minor et al, 2016). The International Union of Crystallography (IUCr) responded by forming the IUCr Diffraction Data Deposition Working Group (DDDWG) in 2011.…”

Section: Introductionmentioning

confidence: 99%

A public database of macromolecular diffraction experiments

Grabowski

Langner

Cymborowski

et al. 2016

Acta Crystallogr D Struct Biol

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109

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The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences. However, there remains no mandate for public disclosure of the original diffraction data. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata. IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability. The resource, which is accessibleviathe web portal at http://www.proteindiffraction.org, can be searched using various criteria. All data are available for unrestricted access and download. The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallographic studies of biological macromolecules. The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics projects.

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“…1/3) 6,7 . Such errors can easily become viral 24 and may confuse, among others, untrained scientists that lack time to fix stereochemical issues.…”

mentioning

confidence: 99%

“…Therefore, we suggest that in the absence of clear experimental or stereochemical evidence, it may be more suitable to not assign any ions in biomolecular structures with insufficient resolutions since those assignments may subsequently be taken for granted by others with the risk to create inappropriate prior knowledge affecting the outcome of database surveys 24 .…”

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confidence: 99%

Deflating the RNA Mg²⁺bubble. Stereochemistry to the rescue!

Auffinger¹,

Ennifar²,

D’Ascenzo³

2020

Preprint

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Proper evaluation of the ionic structure of biomolecular systems remains challenging in X-ray and cryo-EM techniques. Herein, we re-evaluate the model of the ribosome ionic structure proposed in a 2019 Nat. Commun. paper by A. Rozov et al. We establish that neglecting stereochemical principles when evaluating ion binding features results in misleading conceptions of the solvent structure of ribosomal particles. We propose an alternative interpretation of the crystallographic data that suggests that monovalent ions and not divalent ions are prevalent in the 1 st solvation shell of ribosomes. We stress that the use of proper stereochemical guidelines is essential for deflating the current Mg 2+ we witness in many ribosome and other RNA structures.A recent publication by Rozov, Yusupova et al. (Rozov et al. 2019), emphasized that long-wavelength X-ray diffraction techniques can now be used to detect the presence of potassium ions (K +

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Safeguarding Structural Data Repositories against Bad Apples

Cited by 37 publications

References 25 publications

Prior knowledge or freedom of interpretation? A critical look at a recently published classification of “novel” Zn binding sites

Prior knowledge or freedom of interpretation? A critical look at a recently published classification of “novel” Zn binding sites

A public database of macromolecular diffraction experiments

Deflating the RNA Mg²⁺bubble. Stereochemistry to the rescue!

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Safeguarding Structural Data Repositories against Bad Apples

Cited by 37 publications

References 25 publications

Prior knowledge or freedom of interpretation? A critical look at a recently published classification of “novel” Zn binding sites

Prior knowledge or freedom of interpretation? A critical look at a recently published classification of “novel” Zn binding sites

A public database of macromolecular diffraction experiments

Deflating the RNA Mg2+bubble. Stereochemistry to the rescue!

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Product

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Deflating the RNA Mg²⁺bubble. Stereochemistry to the rescue!