@inproceedings{
gong2023binding,
title={Binding Oracle: Fine-Tuning From Stability to Binding Free Energy},
author={Chengyue Gong and Adam Klivans and Jordan Wells and James Loy and qiang liu and Alex Dimakis and Daniel Diaz},
booktitle={NeurIPS 2023 Generative AI and Biology (GenBio) Workshop},
year={2023},
url={https://openreview.net/forum?id=ChU7MCLk1J}
}
The ability to predict changes in binding free energy (▵▵$G_{bind}$) 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 ▵▵$G_{bind}$ 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.
Binding Oracle: Fine-Tuning From Stability to Binding Free Energy
Chengyue Gong Adam Klivans Jordan Wells James Loy qiang liu Alex Dimakis Daniel Diaz