An Interactive Strategy to Visualize Common Subgraphs in Protein-Ligand Interaction

Interactions between proteins and ligands play an important role in biological processes of living systems. For this reason, the development of computational methods to facilitate the understanding of the ligand-receptor recognition process is fundamental, since this comprehension is a major step towards ligand prediction, target identification, lead discovery, among others. This article presents a visual interactive interface to explore protein-ligand interactions and their conserved substructures for a set of similar proteins. The protein-ligand interface is modeled as bipartite graphs, where nodes represents protein and ligand atoms, and edges depicts interactions between them. Such graphs are the input to search for frequent subgraphs that are the conserved interaction patterns over the datasets. To illustrate the potential of our strategy, we used two test datasets, Ricin and human CDK2. Availability: http:// dcc.ufmg.br/similar to alexandrefassio/gremlin/.