Analysis of relevant physicochemical properties in obligate and non-obligate protein-protein interactions

Identification and analysis of types of protein-protein interactions (PPI) is an important problem in molecular biology because of its key role in many biological processes in living cells. In this paper, we focus on obligate and non-obligate complexes, their prediction and analysis. We propose a feature selection scheme called MRMRpro which is based on Minimum Redundancy Maximum Relevance (MRMR) to focus on the most discriminative and relevant properties to distinguish between these two types of complexes. Our prediction approach uses desolvation energies of pairs of atoms or amino acids present in the interfaces of such complexes. Our results on two well-known datasets confirm that MRMRpro leads to significant improvements on performance by finding more relevant features for prediction. Furthermore, the prediction performance of our biologically guided feature selection methods demonstrate that hydrophobic amino acids are more discriminating than hydrophilic and amphipathic amino acids to distinguish between obligate and non-obligate complexes.