Structure-based self-supervised learning enables ultrafast protein stability prediction upon mutation.

Predicting free energy changes (ΔΔG) is essential for enhancing our understanding of protein evolution and plays a pivotal role in protein engineering and pharmaceutical development. While traditional methods offer valuable insights, they are often constrained by computational speed and reliance on biased training datasets. These constraints become particularly evident when aiming for accurate ΔΔG predictions across a diverse array of protein sequences. Herein, we introduce Pythia, a self-supervised graph neural network specifically designed for zero-shot ΔΔG predictions. Our comparative benchmarks demonstrate that Pythia outperforms other self-supervised pretraining models and force field-based approaches while also exhibiting competitive performance with fully supervised models. Notably, Pythia shows strong correlations and achieves a remarkable increase in computational speed of up to 10-fold. We further validated Pythia's performance in predicting the thermostabilizing mutations of limonene epoxide hydrolase, leading to higher experimental success rates. This exceptional efficiency has enabled us to explore 26 million high-quality protein structures, marking a significant advancement in our ability to navigate the protein sequence space and enhance our understanding of the relationships between protein genotype and phenotype. In addition, we established a web server at https://pythia.wulab.xyz to allow users to easily perform such predictions.