A Deep-Learning Approach toward Rational Molecular Docking Protocol Selection
José Jiménez-Luna, Alberto Cuzzolin, Giovanni Bolcato, Mattia Sturlese, Stefano Moro
Abstract
While a plethora of different protein-ligand docking protocols have been developed over the past twenty years, their performances greatly depend on the provided input protein-ligand pair. In this study, we developed a machine-learning model that uses a combination of convolutional and fully connected neural networks for the task of predicting the performance of several popular docking protocols given a protein structure and a small compound. We also rigorously evaluated the performance of our model using a widely available database of protein-ligand complexes and different types of data splits. We further open-source all code related to this study so that potential users can make informed selections on which protocol is best suited for their particular protein-ligand pair.