The fourth MIDD student symposium will take place on January 6th at 2:30 pm in CHEM110 (Chemistry Building). The event will give student affiliated with the MIDD the opportunity to present their work to other UWM students. We hold this event six times a year, bimonthly on the first Wednesday of the month at 2:30 pm. The presentation are 20 minutes long with 5 min Q&A. We have the following presentations:
Learning Protein–Protein Binding Free Energies from Interface Graphs and Physicochemical Descriptors
Qingshu Zhao from the Research Group of Prof. Arjun Saha Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
Predicting protein−protein binding free energy (ΔG) from structure remains a central challenge in computational biophysics. Here, we present our recently published model GULP (Graph-based Unified Learning for Protein binding), a graph neural network (GNN) that jointly learns from a residue-level graph representation of the binding interface and global physicochemical descriptors. We systematically investigate how training data distribution affects model performance by comparing a full training set with a balanced subset enriched for extreme-affinity complexes. GULP is computationally efficient and provides interpretable insights into residue-level and physicochemical contributions to binding. On external validation, GULP achieves a mean absolute error (MAE) of 2.31 kcal/mol and shows moderate agreement with experimental ΔG values (Pearson r = 0.54, Spearman ρ = 0.58).