Efficient Similarity Retrieval of Protein Binding Sites based on Histogram Comparison

We propose a method for comparing protein structures or, more specifically, protein binding sites using a histogram-based representation that captures important geometrical and physico-chemical properties. In comparison to hitherto existing approaches in structural bioinformatics, especially methods from graph theory and computational geometry, our approach is computationally much more efficient. Moreover, despite its simplicity, it appears to capture and recover functional similarities surprisingly well.