There is an interesting publication in the latest issue of Chemical Biology and Drug Design describing, Chem-Path-Tracker An automated tool to analyze chemical motifs in molecular structures DOI. This is a plugin for the molecular visualisation tool VMD that allows the user to highlight and reveal potential chemical motifs with a protein using only a few selections.
The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed Chem-Path-Tracker.
More details on the project page