GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison

Initial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close in the 3-dimensional (3D) structure, 3D contact approaches can complement sequence approaches. Traditional 3D contact approaches study 3D structures directly and are alignment-based. Instead, 3D structures can be modeled as protein structure networks (PSNs). Then, network approaches can compare proteins by comparing their PSNs. These can be alignment-based or alignment-free. We focus on the latter. Existing network alignment-free approaches have drawbacks: 1) They rely on naive measures of network topology. 2) They are not robust to PSN size. They cannot integrate 3) multiple PSN measures or 4) PSN data with sequence data, although this could improve comparison because the different data types capture complementary aspects of the protein structure. We address this by: 1) exploiting well-established graphlet measures via a new network alignment-free approach, 2) introducing normalized graphlet measures to remove the bias of PSN size, 3) allowing for integrating multiple PSN measures, and 4) using ordered graphlets to combine the complementary PSN data and sequence (specifically, residue order) data. We compare synthetic networks and real-world PSNs more accurately and faster than existing network (alignment-free and alignment-based), 3D contact, or sequence approaches.