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Workshop: Machine Learning in Structural Biology Workshop

Binding Oracle: Fine-Tuning From Stability to Binding Free Energy

Chengyue Gong · Adam Klivans · Jordan Wells · James Loy · Qiang Liu · Alex Dimakis · Daniel Diaz


The ability to predict changes in binding free energy (ddG binding) for mutations at protein-protein interfaces (PPIs) is critical for the understanding genetic diseases and engineering novel protein-based therapeutics. Here, we present Binding Oracle: a structure-based graph transformer for predicting ddG binding at PPIs. Binding Oracle fine-tunes Stability Oracle with Selective LoRA: a technique that synergizes layer selection via gradient norms with LoRA. Selective LoRA enables the identification and fine-tuning of the layers most critical for the downstream task, thus, regularizing against overfitting. Additionally, we present new training-test splits of mutational data from the SKEMPI2.0, Ab-Bind, and NABE databases that use a strict 30% sequence similarity threshold to avoid data leakage during model evaluation. Binding Oracle, when trained with the Thermodynamic Permutations data augmentation technique, achieves SOTA on S487 without using any evolutionary auxiliary features. Our results empirically demonstrate how sparse fine-tuning techniques, such as Selective LoRA, can enable rapid domain adaptation in protein machine learning frameworks.

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