Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction

Shitong Luo, Yufeng Su, Zuofan Wu, Chenpeng Su, Jian Peng, Jianzhu Ma

Keywords: effect of mutations, protein-protein interaction, unsupervised learning

Abstract: Protein-protein interactions are crucial to many biological processes, and predicting the effect of amino acid mutations on binding is important for protein engineering. While data-driven approaches using deep learning have shown promise, the scarcity of annotated experimental data remains a major challenge. In this work, we propose a new approach that predicts mutational effects on binding using the change in conformational flexibility of the protein-protein interface. Our approach, named Rotamer Density Estimator (RDE), employs a flow-based generative model to estimate the probability distribution of protein side-chain conformations and uses entropy to measure flexibility. RDE is trained solely on protein structures and does not require the supervision of experimental values of changes in binding affinities. Furthermore, the unsupervised representations extracted by RDE can be used for downstream neural network predictions with even greater accuracy. Our method outperforms empirical energy functions and other machine learning-based approaches.

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