Abstract
Recent papers highlight the presence of large numbers of compressed angles in metal ion coordination geometries for metalloprotein entries in the worldwide Protein Data Bank, due mainly to multidentate coordination. The prevalence of these compressed angles has raised the controversial idea that significantly populated aberrant or even novel coordination geometries may exist. Some of these papers have undergone severe criticism, apparently due to views held that only canonical coordination geometries exist in significant numbers. While criticism of controversial ideas is warranted and to be expected, we believe that a line was crossed where unfair criticism was put forth to discredit an inconvenient result that compressed angles exist in large numbers, which does not support the dogmatic canonical coordination geometry view. We present a review of the major controversial results and their criticisms, pointing out both good suggestions that have been incorporated in new analyses, but also unfair criticism that was put forth to support a particular view. We also suggest that better science is enabled through: (i) a more collegial and collaborative approach in future critical reviews and (ii) the requirement for a description of methods and data including source code and visualizations that enables full reproducibility of results.
Document Type
Article
Publication Date
5-2017
Digital Object Identifier (DOI)
https://doi.org/10.1002/prot.25263
Funding Information
This work was supported in part by National Science Foundation NSF 1252893 (Hunter N.B. Moseley) and NIH 1U24DK097215-01A1 (Richard M. Higashi, Teresa W.-M. Fan, Andrew N. Lane, and Hunter N.B. Moseley). ECR is supported by grant P20GM103436 (Nigel Cooper, PI).
Related Content
Software and results available at: http://software.cesb.uky.edu, https://doi.org/10.6084/m9.figshare.4229297, and https://doi.org/10.6084/m9.figshare.4229333
Additional Supporting Information may be found in the online version of this article.
Repository Citation
Yao, Sen; Flight, Robert M.; Rouchka, Eric C.; and Moseley, Hunter N. B., "Perspectives and Expectations in Structural Bioinformatics of Metalloproteins" (2017). Molecular and Cellular Biochemistry Faculty Publications. 170.
https://uknowledge.uky.edu/biochem_facpub/170
Supporting Information
Notes/Citation Information
Published in Proteins, v. 85, issue 5, p. 938-944.
© 2017 Wiley Periodicals, Inc.
The copyright holder has granted the permission for posting the article here.
This is the peer reviewed version of the following article: Yao, S., Flight, R. M., Rouchka, E. C., & Moseley, H. N. B. (2017). Perspectives and expectations in structural bioinformatics of metalloproteins. Proteins, 85(5), 938-944, which has been published in final form at https://doi.org/10.1002/prot.25263. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.