METALizer

Overview

METALizer predicts the coordination geometry of metal ions in metalloproteins. Users can compare potential coordination geometries to those found in the examined structure. The predicted coordination geometries and the observed metal interaction distances can be interactively compared to statistics calculated based on the PDB.

Furthermore, other tools of the NAOMI ChemBio Suite are part of METALizer:

Using SIENA, ensembles of proteins with sequentially and structurally closely related metal binding sites can be retrieved from the PDB, superimposed, and visualized. The superposition enables users to compare predicted coordination geometries and metal interaction distances to those calculated only for related metal binding sites. Furthermore, users can explore differing binding modes of metal ions regarding ligands and proteins.

Using EDIAscorer, atoms that are poorly supported by electron density are excluded from the METALizer analyses.

Software Availability

We are offering METALizer as part of our ProteinsPlus web service. Please visit https://proteins.plus, upload your protein, and choose METALizer.

References

Schöning-Stierand, K.; Diedrich, K.; Fährrolfes, R.; Flachsenberg, F.; Meyder, A.; Nittinger, E.; Steinegger, R.; Rarey, M. ProteinsPlus: interactive analysis of protein-ligand binding interfaces. Nucleic Acids Res 2020, 48 (W1), W48-W53. DOI: https://doi.org/10.1093/nar/gkaa235