authors: Alexandre V. Fassio, Lucianna H. S. Santos, Sabrina A. Silveira, Rafaela S. Ferreira and Raquel C. de Melo-Minardi
Extremely important roles on biological systems depend on protein-ligand interactions. Investigating the processes involved in such interactions contributes significantly to understand how molecular recognition occurs and to ligand prediction, target identification, lead discovery and drug design. Nowadays, a large-scale dataset of protein-ligand complexes is available in the Protein Data Bank, what lead several tools to be proposed as an effort to investigate and depict protein-ligand interactions. However, none of them presents large-scale statistical, visual and interactive analysis of conserved protein-ligand interactions. We developed nAPOLI (Analysis of PrOtein-Ligand Interactions), which is a set of algorithms to detect conserved interactions in labeled bigraphs of protein-ligand interactions at atomic-level and a powerful interactive web server that enable users to use these algorithms to analyse their molecular data. nAPOLI was designed to allow a large-scale analysis and present results using visual strategies. We validated our methods and results by comparing nAPOLI and two well-known tools: CREDO and LIGPLOT. Finally, we illustrate, with a virtual screening ligand selection example, how nAPOLI can have a wide use in structural biology community.