AlphaFold for Docking Screens

AlphaFold is an AI system developed by Google DeepMind to generate three-dimensional structures of proteins without experimental data. The models created with AlphaFold are available on the AlphaFold Protein Structure Database (AlphaFoldDB) ( https://alphafold.ebi.ac.uk/ ). The AlphaFold database is searchable by sequence and protein identification. This chapter focuses on an AlphaFold model and its use for docking screens using Molegro Virtual Docker. We rely on Jupyter Notebooks to integrate docking simulations and build regression models based on the atomic coordinates of protein-pose complexes. Our study focuses on constructing a neural network regression model to predict the inhibition of cyclin-dependent kinase 19 (CDK19). This enzyme is a target for anticancer drugs and does not have experimental data for its atomic coordinates. We utilize the Molegro Data Modeller to construct a regression model based on docking results of inhibitors for which binding affinity data is available. All CDK19 datasets and Jupyter Notebooks discussed in this work are available at GitHub: https://github.com/azevedolab/docking#readme .