Similarity measures for protein structures based on fuzzy histogram comparison

We propose a method for comparing protein structures or, more specifically, protein binding sites in terms of histogram-based representations. These representation are intended to capture important geometrical and physico-chemical properties. In comparison to hitherto existing approaches in structural bioinformatics, especially graph-based methods and methods from computational geometry, our approach is computationally much more efficient. Moreover, despite its simplicity, first experimental studies suggest that it is able to produce useful measures of similarity.