Perspectives and expectations in structural bioinformatics of metalloproteins.
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. Proteins 2017; 85:938-944. © 2016 Wiley Periodicals, Inc.
School of Interdisciplinary and Graduate Studies, University of Louisville, Louisville, Kentucky, 40292.|Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky, 40292.|Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, 40356.|Markey Cancer Center, University of Kentucky, Lexington, Kentucky, 40356.|Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, Kentucky, 40356.
Sen
S
Yao
Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, 40356.|Markey Cancer Center, University of Kentucky, Lexington, Kentucky, 40356.|Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, Kentucky, 40356.
Robert M
RM
Flight
School of Interdisciplinary and Graduate Studies, University of Louisville, Louisville, Kentucky, 40292.|Department of Computer Engineering and Computer Science, University of Louisville, Louisville, Kentucky, 40292.
Eric C
EC
Rouchka
Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, 40356.|Markey Cancer Center, University of Kentucky, Lexington, Kentucky, 40356.|Center for Environmental and Systems Biochemistry, University of Kentucky, Lexington, Kentucky, 40356.
Hunter N B
0000-0003-3995-5368
HN
Moseley
D019295:Computational Biology / Q000941:ethics* / Q000639:trends; D056831:Coordination Complexes / Q000737:chemistry*; D030562:Databases, Protein; D006801:Humans; D033181:Information Dissemination / Q000941:ethics*; D008667:Metalloproteins / Q000737:chemistry*; D008670:Metals / Q000737:chemistry*; D011487:Protein Conformation; D015203:Reproducibility of Results
D056831:Coordination Complexes; D008667:Metalloproteins; D008670:Metals
canonical coordination geometry; collaboration vs. competition; compressed angles; data sharing; metal coordination