Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server

Nat Protoc. 2014 Jan;9(1):156-70. doi: 10.1038/nprot.2013.172. Epub 2013 Dec 19.


Metals have vital roles in both the mechanism and architecture of biological macromolecules. Yet structures of metal-containing macromolecules in which metals are misidentified and/or suboptimally modeled are abundant in the Protein Data Bank (PDB). This shows the need for a diagnostic tool to identify and correct such modeling problems with metal-binding environments. The CheckMyMetal (CMM) web server ( is a sophisticated, user-friendly web-based method to evaluate metal-binding sites in macromolecular structures using parameters derived from 7,350 metal-binding sites observed in a benchmark data set of 2,304 high-resolution crystal structures. The protocol outlines how the CMM server can be used to detect geometric and other irregularities in the structures of metal-binding sites, as well as how it can alert researchers to potential errors in metal assignment. The protocol also gives practical guidelines for correcting problematic sites by modifying the metal-binding environment and/or redefining metal identity in the PDB file. Several examples where this has led to meaningful results are described in the ANTICIPATED RESULTS section. CMM was designed for a broad audience--biomedical researchers studying metal-containing proteins and nucleic acids--but it is equally well suited for structural biologists validating new structures during modeling or refinement. The CMM server takes the coordinates of a metal-containing macromolecule structure in the PDB format as input and responds within a few seconds for a typical protein structure with 2-5 metal sites and a few hundred amino acids.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Binding Sites*
  • Computational Biology / methods*
  • Crystallography, X-Ray
  • Databases, Protein
  • Internet*
  • Metals / chemistry*
  • Nuclear Magnetic Resonance, Biomolecular
  • Sequence Analysis, Protein
  • Software*


  • Metals