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A Geometric Deep Learning Approach to Predict Binding Conformations of Bioactive Molecules
preprintsubmitted on 20.04.2021, 11:30 and posted on 20.04.2021, 13:24 by Oscar Méndez-Lucio, Mazen Ahmad, Ehecatl Antonio del Rio-Chanona, Jörg Kurt Wegner
Understanding the interactions formed between a ligand and its molecular target is key to guide the optimization of molecules. Different experimental and computational methods have been key to understand better these intermolecular interactions. Herein, we report a method based on geometric deep learning that is capable of predicting the binding conformations of ligands to protein targets. Concretely, the model learns a statistical potential based on distance likelihood which is tailor-made for each ligand-target pair. This potential can be coupled with global optimization algorithms to reproduce experimental binding conformations of ligands. We show that the potential based on distance likelihood described in this paper performs similar or better than well-established scoring functions for docking and screening tasks. Overall, this method represents an example of how artificial intelligence can be used to improve structure-based drug design.