_MSE_: The Metal-binding Site Evaluator. Performs a full analysis on a user submitted PDB structure, generating a complete report of the metal-binding sites, their geometry, first and second shell ligands, hydrogen-bond interactions, etc. Uses our *MSIT* java application. _ClusterGeom_: Java application that performs a geometrical analysis of iron-sulfur clusters ([4Fe4S] and [3Fe4S]). Generates parameters and projections that can be correlated with cluster distortion from an ideal geometry. Expansion of the analytical tools, to include: Chi angle distributions and 2D comparisons, Bond angle distributions, Liganding pattern and parameter distribution correlations, etc.