Study of interface residue pairs is important for understanding the interactions between monomers inside a trimer protein–protein complex. We developed a two-layer support vector machine (SVM) ensemble-classifier that considers physicochemical and geometric properties of amino acids and the influence of surrounding amino acids. Different descriptors and different combinations may give different prediction results. We propose feature combination engineering based on correlation coefficients and F-values. The accuracy of our method is 65.38% in independent test set, indicating biological significance. Our predictions are consistent with the experimental results. It shows the effectiveness and reliability of our method to predict interface residue pairs of protein trimers.

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Protein-protein interactions play an important role in life activities. The study of protein-protein interactions helps to better understand the mechanism of protein complex interaction, which is crucial for drug design, protein function annotation and three-dimensional structure prediction of protein complexes. In this paper, we study the tetramer protein complex interaction. The research has two parts: The first part is to predict the interaction between chains of the tetramer protein complex. In this part, we proposed a feature map to represent a sample generated by two chains of the tetramer protein complex, and constructed a Convolutional Neural Network (CNN) model to predict the interaction between chains of the tetramer protein complex. The AUC value of testing set is 0.6263, which indicates that our model can be used to predict the interaction between chains of the tetramer protein complex. The second part is to predict the tetramer protein complex interface residue pairs. In this part, we proposed a Support Vector Machine (SVM) ensemble method based on under-sampling and ensemble method to predict the tetramer protein complex interface residue pairs. In the top 10 predictions, when at least one protein-protein interaction interface is correctly predicted, the accuracy of our method is 82.14%. The result shows that our method is effective for the prediction of the tetramer protein complex interface residue pairs.