GReMLIN: A Graph Mining Strategy to Infer Protein-Ligand Interaction Patterns

Abstract

Interactions between proteins and ligands are relevant in many biological processes. In the last years, such interactions have gained even more attention as the comprehension of protein-ligand molecular recognition is an important step to ligand prediction, target identificantion, and drug design, among others. This article presents GReMLIN (Graph Mining strategy to infer protein-Ligand INteraction patterns), a strategy to search for conserved protein-ligand interactions in a set of related proteins, based on frequent subgraph mining, that is able to perceive structural arrangements relevant for protein-ligand interaction. When compared to experimentally determined interactions, our in silico strategy was able to find many of relevant binding site residues/atoms for CDK2 and active site residues/atoms for Ricin.