Application of Network Theory in Understanding and Predicting Protein Structure and Function

Elucidating protein structure and function relationships from sequence data, and predicting protein structure and function by an automatic, high-throughput means pose important and imminent challenges for structural proteomics. In recent years, there has been growing interest in applying network concepts and theory to meet this challenge. The network approach transforms a protein structure into a network by representing each amino acid residue as a node and each residue-residue interaction with an edge connecting two residues. Through this transformation, insights into various aspects of protein structure and function are explored from the perspective of networks. Current applications of the network approach include: understanding protein stability, studying protein folding, developing scoring functions for structure discrimination, predicting protein functional sites and analyzing protein-protein and protein-DNA complexes. The network approach is computationally efficient and proves to be a useful tool in structural proteomics. This review covers the applications of the network approach in the field of structural proteomics.