SGPocket: A New Graph Convolutional Neural Network for Ligand-protein Binding Site Prediction

Abstract

Background: Drug research is a long process, taking more than 10 years and requiring considerable financial resources. Therefore, researchers and industrials aim to reduce time and cost. Thus, they use computational simulations like molecular docking to explore huge databases of compounds and extract the most promising ones for further tests. Structure-based molecular docking is a complex process mixing surface exploration and energy computation to find the minimal free energy of binding corresponding to the best interaction location.

Objective: Our work is developed in the ligand-protein context, where ligands are small compounds like drugs. In most cases, no information is known about where on the protein surface the ligand will bind. Thus, the whole protein surface must be explored, which takes a huge amount of time.

Methods: We have developed SGPocket (meaning Spherical Graph Pocket), a binding site prediction method. Our method allows us to reduce the explored protein surface using deep learning without any information about a ligand. SGPocket uses the spherical graph convolutional operator working on a spherical relative positioning of amino acids in the protein. Then, a final step of clustering extracts the binding sites.

Results: Tested and compared (with well-known binding site prediction methods) on a hand-made dataset, our method performed well and can reduce the docking computing time.

Conclusion: Thus, SGPocket allows the reduction of the exploration surface in the molecular docking process by restricting the simulation only to the site(s) predicted to be interesting.

Keywords: Artificial Intelligence; Binding site prediction; Deep Learning; Graph Neural Network; Molecular Docking; Protein-Ligand.