Similarity Analysis of Protein Binding Sites: A Generalization of the Maximum Common Subgraph Measure Based on Quasi-Clique Detection

Protein binding sites are often represented by means of graphs capturing their most important geometrical and physicochemical properties. Searching for structural similarities and identifying functional relationships between them can thus be reduced to matching their corresponding graph descriptors. In this paper, we propose a method for the structural analysis of protein binding sites that makes use of such matching techniques to assess the similarity between proteins independently of sequence or fold homology. More specifically, we propose a similarity measure that generalizes the commonly used maximum common subgraph measure in two ways. First, using algorithms for so-called quasi-clique detection, our measure is based on maximum ‘approximately’ common subgraphs, a relaxation of maximum common subgraphs which is tolerant toward edge mismatches. Second, instead of focusing on equivalence, our measure is a compromise between a generalized equivalence and an inclusion measure. An experimental study is presented to illustrate the effectiveness of the method and to show that both types of relaxation are useful in the context of protein structure analysis.