The Downside and Upside of Including Backbone Flexibility for Predicting Protein and Antibody Binding

In this study we will address the following issues: 1. Can we adapt our coarse-grained folding algorithm, Upside, to predict binding? 2. What kinds of interactions are important for binding compared to folding? 3. What level of coarse graining can be tolerated? 4. Under what conditions backbone flexibility can hinder or help the docking process? 5. Is predicting folding or binding harder? We achieved substantially greater predictive performance on protein-protein docking through new potential energy terms for binding and training of our force field on a docking benchmark set, and are comptetive with established methods.