Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.
Acta Crystallogr D Struct Biol. 2017 Mar 1;73(Pt 3):223-233. doi: 10.1107/S2059798317001061. Epub 2017 Feb 22.
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.
金属在许多生物过程中是必不可少的，并且在蛋白质数据库（PDB）中约有 40%的大分子结构中模拟了金属离子。然而，这些结构中有很大一部分含有建模不佳的金属结合位点。CheckMyMetal（CMM）是一个易于使用的用于大分子的金属结合位点验证服务器，可在 http://csgid.org/csgid/metal_sites 免费获得。CMM 服务器可以检测到不正确的金属分配以及金属结合位点的几何形状和其他不规则性。通过按金属类型分组的几个实际示例说明了大分子中金属位点建模和验证的准则。这些示例向 CMM 用户（和一般的晶体学家）展示了他们在为特定金属离子建模时可能遇到的问题。
