R2V-PPI: Enhancing Prediction of Protein-Protein Interactions Using Word2Vec Embeddings and Deep Neural Networks

Proteins play a crucial role in living organisms, and understanding protein-protein interactions is vital for comprehending their functions and aiding drug discovery. In recent years, advanced deep learning models have been developed to predict protein-protein interactions from sequences. However, these large-scale approaches often suffer from deficiencies, resulting in both false positive and false negative predictions. Traditional encoding methods struggle to effectively represent the semantic meaning of individual residues in protein sequences and their impact on neighbouring residues. To overcome these deficiencies, we propose a novel method named R2V-PPI (Residue-to-Vector embeddings based Protein-Protein Interaction Framework) that effectively represents protein sequences and predicts protein-protein interactions. Inspired by Word2Vec, R2V-PPI learns informative representations of individual amino acid residues, capturing the context and relationships between them in raw protein sequences. These representations provide valuable input features for a downstream deep learning model. Our methodology offers a robust and versatile approach for predicting protein-protein interactions, especially when structural information is limited or unavailable. Evaluation on the S. cerevisiae dataset demonstrates that R2V-PPI outperforms existing state-of-the-art machine learning models.