Protein-Protein Interaction Interface Residue Pair Prediction Based on Deep Learning Architecture

Motivation: Proteins usually fulfill their biological functions by interacting with other proteins. Although some methods have been developed to predict the binding sites of a monomer protein, these are not sufficient for prediction of the interaction between two monomer proteins. The correct prediction of interface residue pairs from two monomer proteins is still an open question and has great significance for practical experimental applications in the life sciences. We hope to build a method for the prediction of interface residue pairs that is suitable for those applications. Results: Here, we developed a novel deep network architecture called the multi-layered Long-Short Term Memory networks (LSTMs) approach for the prediction of protein interface residue pairs. First, we created three new descriptions and used other six worked characterizations to describe an amino acid, then we employed these features to discriminate between interface residue pairs and non-interface residue pairs. Second, we used two thresholds to select residue pairs that are more likely to be interface residue pairs. Furthermore, this step increases the proportion of interface residue pairs and reduces the influence of imbalanced data. Third, we built deep network architectures based on Long-Short Term Memory networks algorithm to organize and refine the prediction of interface residue pairs by employing features mentioned above. We trained the deep networks on dimers in the unbound state in the international Protein-protein Docking Benchmark version 3.0. The updated data sets in the versions 4.0 and 5.0 were used as the validation set and test set respectively. For our best model, the accuracy rate was over 62 percent when we chose the top 0.2 percent pairs of every dimer in the test set as predictions, which will be very helpful for the understanding of protein-protein interaction mechanisms and for guidance in biological experiments.