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J Chem Inf Model. 2013 Nov 25;53(11):3064-75. doi: 10.1021/ci400459w. Epub 2013 Oct 28.

MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids.

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Magnetic Resonance Center (CERM) - University of Florence , Via L. Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.


We developed a new software tool, MetalS(2), for the structural alignment of Minimal Functional Sites (MFSs) in metal-binding biological macromolecules. MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. On our example data sets, MetalS(2) unveiled structural similarities that other programs for protein structure comparison do not consistently point out and overall identified a larger number of structurally similar MFSs. MetalS(2) supports the comparison of MFSs harboring different metals and/or with different nuclearity and is available both as a stand-alone program and a Web tool (

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