Improving scoring functions for protein-protein docking with LambdaLoss

Richard Zhu, Darren Xu, Lee-Shin Chu, Jeffrey J. Gray

Modeling protein-protein interactions requires accurate scoring functions that can rank potential poses (conformations) of a protein-protein complex to differentiate near-native poses from incorrect ones. Here, we propose a general framework for improving protein-protein pose ranking and other biomolecular interaction models using the LambdaLoss loss function from the Learning-to-Rank field. We test this framework by fine-tuning the energy prediction head of DFMDock with the LambdaLoss on an augmented dataset of 2.9M decoy poses derived from the DIPS dataset. On targets from the CAPRI score set benchmark, our fine-tuned ranking model LambdaDockScore is better at identifying correct poses in its top-1 and top-5 predictions compared to EuDockScore, a state-of-the-art method. LambdaDockScore also improves upon baseline DFMDock ranking performance for scoring antibody-antigen complexes and protein-protein complexes with very large or small binding interfaces.