Integrating Structural Information: Comparing Classification-Based and Segmentation-Based Predictors in Bioinformatics (Case Study: Protein-Peptide Region Residue-Level Interaction) Using Structural Information

Understanding the regions where proteins bind to peptides is vital for studying diseases like cancer, as it sheds light on various cellular processes and aids in drug discovery. Although researchers can experimentally investigate protein-peptide interactions at the region level by analyzing the structures of their complexes, only a limited number of these structures are known. Additionally, experiments to determine these interactions can be both costly and time-consuming. Computational methods provide an alternative and complementary approach to experimental techniques. As a result, using computational methods to predict peptide-binding regions can significantly enhance the efficiency and cost-effectiveness of experimental research. To leverage these advantages, this study introduces a new method named Structure-based Prediction of Residue-level Interaction of Peptides (SPRINT-Pep), designed to pinpoint the binding regions between proteins and peptides. This approach leverages two distinct predictive models: a classification-based model combining DeepResNet with a Support Vector Machine (SVM) and a segmentation-based model called DeepU-Net. Our predictions outperform other state-of-the-art methods in terms of F-measures (by at least 23%), precision (by at least 3.7%), and the balance between sensitivity and specificity (by about 7.7%). These findings demonstrate the proficiency of the proposed method.