Protein Docking Model Evaluation by 3D Deep Convolutional Neural Networks

We developed a convolutional deep neural network-based approach named DOVE (DOcking decoy selection with Voxel-based deep neural nEtwork) for evaluating protein docking models. To evaluate a protein docking model, DOVE scans the protein-protein interface of the model with a 3D voxel and considers atomic interaction types and their energetic contributions as input features applied to the neural network. The deep learning models were trained and validated on docking models available in the ZDock and DockGround databases. Among the different combinations of features tested, almost all outperformed existing scoring functions.