Abstract
Protein structure determines function, and structural information is critical for predicting protein thermostability. This study proposes a novel method for protein thermostability prediction by integrating graph embedding features and network topological features. By constructing residue interaction networks (RINs) to characterize protein structures, we calculated network topological features and utilize deep neural networks (DNN) to mine inherent characteristics. Using DeepWalk and Node2vec algorithms, we obtained node embeddings and extracted graph embedding features through a TopN strategy combined with bidirectional long short-term memory (BiLSTM) networks. Additionally, we introduced the Doc2vec algorithm to replace the Word2vec module in graph embedding algorithms, generating graph embedding feature vector encodings. By employing an attention mechanism to fuse graph embedding features with network topological features, we constructed a high-precision prediction model, achieving 87.85% prediction accuracy on a bacterial protein dataset. Furthermore, we analyzed the differences in the contributions of network topological features in the model and the differences among various graph embedding methods, and found that the combination of DeepWalk features with Doc2vec and all topological features was crucial for the identification of thermostable proteins. This study provides a practical and effective new method for protein thermostability prediction, and at the same time offers theoretical guidance for exploring protein diversity, discovering new thermostable proteins, and the intelligent modification of mesophilic proteins.