Fig. 8: Ligand binding site definition algorithm.
The method defines ligand binding sites from a set of three-dimensional structures portraying the complex of a protein of interest bound to ligands. a Protein–ligand complex (P18031). b Ligand binding fingerprint, comprised by protein residue numbers interacting with ligand. c Formula of the similarity metric: relative intersection, Irel. d Hierarchical clustering tree resulting from the similarity matrix, cut at threshold to determine distinct clusters of ligands. e Three-dimensional structure of all ligands binding to protein, coloured according to the cluster they group into. Only ligands found clusters 1–7 are in coloured based on their cluster membership. The rest are coloured in grey. The tree on (d) represents only a part of the tree, showing 7/18 binding sites defined on P18031. This is represented by a dash line pointing downwards on the tree.
