Prediction of the Trimer Protein Interface Residue Pair by CNN-GRU Model Based on Multi-Feature Map

Most life activities of organisms are realized through protein-protein interactions, and these interactions are mainly achieved through residue-residue contact between monomer proteins. Consequently, studying residue-residue contact at the protein interaction interface can contribute to a deeper understanding of the protein-protein interaction mechanism. In this paper, we focus on the research of the trimer protein interface residue pair. Firstly, we utilize the amino acid k-interval product factor descriptor (AAIPF(k)) to integrate the positional information and physicochemical properties of amino acids, combined with the electric properties and geometric shape features of residues, to construct an 8 × 16 multi-feature map. This multi-feature map represents a sample composed of two residues on a trimer protein. Secondly, we construct a CNN-GRU deep learning framework to predict the trimer protein interface residue pair. The results show that when each dimer protein provides 10 prediction results and two protein-protein interaction interfaces of a trimer protein needed to be accurately predicted, the accuracy of our proposed method is 60%. When each dimer protein provides 10 prediction results and one protein-protein interaction interface of a trimer protein needs to be accurately predicted, the accuracy of our proposed method is 93%. Our results can provide experimental researchers with a limited yet precise dataset containing correct trimer protein interface residue pairs, which is of great significance in guiding the experimental resolution of the trimer protein three-dimensional structure. Furthermore, compared to other computational methods, our proposed approach exhibits superior performance in predicting residue-residue contact at the trimer protein interface.