Theoretical and Computational Chemistry

A Deep-Learning Approach Toward Rational Molecular Docking Protocol Selection

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 work we have 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 evaluate 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 guesses on which protocol is best suited for their particular protein-ligand pair.

Content

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Supplementary material

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