Rigid Protein-Protein Docking via Equivariant Elliptic-Paraboloid Interface Prediction
This addresses the problem of accelerating protein-protein docking for applications like drug design and protein engineering, though it is incremental as it builds on existing learning-based methods.
The paper tackles rigid protein-protein docking by proposing ElliDock, a learning-based method that predicts elliptic paraboloid interfaces to represent docking surfaces, achieving the fastest inference time and competitive performance with state-of-the-art models like DiffDock-PP and Multimer, especially in antibody-antigen docking.
The study of rigid protein-protein docking plays an essential role in a variety of tasks such as drug design and protein engineering. Recently, several learning-based methods have been proposed for the task, exhibiting much faster docking speed than those computational methods. In this paper, we propose a novel learning-based method called ElliDock, which predicts an elliptic paraboloid to represent the protein-protein docking interface. To be specific, our model estimates elliptic paraboloid interfaces for the two input proteins respectively, and obtains the roto-translation transformation for docking by making two interfaces coincide. By its design, ElliDock is independently equivariant with respect to arbitrary rotations/translations of the proteins, which is an indispensable property to ensure the generalization of the docking process. Experimental evaluations show that ElliDock achieves the fastest inference time among all compared methods and is strongly competitive with current state-of-the-art learning-based models such as DiffDock-PP and Multimer particularly for antibody-antigen docking.