The DOI matches its Crossref record; 49 of the 49 references it cites were found in a registry or an index.
CheckMyMetal: a macromolecular metal-binding validation tool
Open accessAbstract
Metals are essential in many biological processes, and metal ions are modeled in roughly 40% of the macromolecular structures in the Protein Data Bank (PDB). However, a significant fraction of these structures contain poorly modeled metal-binding sites.CheckMyMetal(CMM) is an easy-to-use metal-binding site validation server for macromolecules that is freely available at http://csgid.org/csgid/metal_sites. The CMM server can detect incorrect metal assignments as well as geometrical and other irregularities in the metal-binding sites. Guidelines for metal-site modeling and validation in macromolecules are illustrated by several practical examples grouped by the type of metal. These examples show CMM users (and crystallographers in general) problems they may encounter during the modeling of a specific metal ion.
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Copper Active Sites in Biology
Solomon, E. I., Heppner, D. E., Johnston, E. M., Ginsbach, J. W., Cirera, J., Qayyum, M., Kieber-Emmons, M. T., Kjaergaard, C. H., Hadt, R. G., & Tian, L. (2014) · Chemical Reviews · doi:10.1021/cr400327t · Cited by 1,751
Metal ion-catalyzed oxidation of proteins: Biochemical mechanism and biological consequences
Stadtman, E. R. (1990) · Free Radical Biology and Medicine · doi:10.1016/0891-5849(90)90006-5 · Cited by 1,153
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Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions
Brown, A., Long, F., Nicholls, R. A., Toots, J., Emsley, P., & Murshudov, G. (2015) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s1399004714021683 · Cited by 618
Multiplicity of metal ion binding patterns to nucleobases
Lippert, B. (2000) · Coordination Chemistry Reviews · doi:10.1016/s0010-8545(00)00260-5 · Cited by 430
Effects of Sodium Ions on DNA Duplex Oligomers: Improved Predictions of Melting Temperatures
Owczarzy, R., You, Y., Moreira, B. G., Manthey, J. A., Huang, L., Behlke, M. A., & Walder, J. A. (2004) · Biochemistry · doi:10.1021/bi034621r · Cited by 332
The Metallobiochemistry of Zinc Enzymes
Vallee, B. L., & Galdes, A. (1984) · Advances in Enzymology - and Related Areas of Molecular Biology · doi:10.1002/9780470123027.ch5 · Cited by 310
Data mining of metal ion environments present in protein structures
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Self-citationValidation of metal-binding sites in macromolecular structures with the CheckMyMetal web server
Zheng, H., Chordia, M. D., Cooper, D. R., Chruszcz, M., Müller, P., Sheldrick, G. M., & Minor, W. (2014) · Nature Protocols · doi:10.1038/nprot.2013.172 · Cited by 304
Self-citationMetal–ligand geometry relevant to proteins and in proteins: sodium and potassium
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Cited by
Wehrspan, Z. J., McDonnell, R. T., & Elcock, A. H. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167377 · Cited by 45
Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins
(2022) · doi:10.1038/s41467-022-31564-1 · Cited by 45
Leonarski, F., D'Ascenzo, L., & Auffinger, P. (2019) · RNA · doi:10.1261/rna.068437.118 · Cited by 39
Ion selectivity and rotor coupling of the Vibrio flagellar sodium-driven stator unit
Hu, H., Popp, P. F., Santiveri, M., Roa-Eguiara, A., Yan, Y., Martin, F. J. O., Liu, Z., Wadhwa, N., Wang, Y., Erhardt, M., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39899-z · Cited by 37
Deflating the RNA Mg 2+ bubble: stereochemistry to the rescue!
Auffinger, P., Ennifar, E., & D'Ascenzo, L. (2021) · RNA · doi:10.1261/rna.076067.120 · Cited by 29
Metadata
- Authors
- Zheng, H., Cooper, D. R., Porebski, P. J., Shabalin, I. G., Handing, K. B., & Minor, W.
- Venue
- Acta Crystallographica Section D Structural Biology
- Published
- 2017-02-22
- Volume
- 73
- Issue
- 3
- Pages
- 223-233
- ISSN
- 2059-7983 (ISSN-L)
- OpenAlex
- W2589875042
- Cited by
- 326
- References
- 49
- FWCI
- 14.00
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Zheng, H., Cooper, D. R., Porebski, P. J., Shabalin, I. G., Handing, K. B., & Minor, W. (2017). CheckMyMetal: a macromolecular metal-binding validation tool. Acta Crystallographica Section D Structural Biology. https://doi.org/10.1107/s2059798317001061
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