GDockScore: a graph-based protein-protein docking scoring function

Protein complexes play vital roles in a variety of biological processes such as mediating biochemical reactions, the immune response, and cell signalling, with three-dimensional structure specifying function. Computational docking methods provide a means to determine the interface between two complexed polypeptide chains without using time-consuming experimental techniques. The docking process requires the optimal solution to be selected with a scoring function. Here we propose a novel graph-based deep learning model that utilizes mathematical graph representations of proteins to learn a scoring function (GDockScore). GDockScore was pre-trained on docking outputs generated with the Protein Data Bank (PDB) biounits and the RosettaDock protocol, and then fine-tuned on HADDOCK decoys generated on the ZDOCK Protein Docking Benchmark. GDockScore performs similarly to the Rosetta scoring function on docking decoys generated using the RosettaDock protocol. Furthermore, state-of-the-art is achieved on the CAPRI score set, a challenging dataset for developing docking scoring functions.