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MOTIVATION The identification of binding hotspots in protein-RNA interactions is crucial for understanding their potential recognition mechanisms and drug design. The experimental methods have many limitations, since they are usually time-consuming and labor-intensive. Thus, developing an effective and efficient theoretical method is urgently needed. RESULTS Here we present SREPRHot, a method to predict hotspots, defined as the residues whose mutation to alanine generate a binding free energy change ≥ 2.0 kcal/mol, while others use a cutoff of 1.0 kcal/mol to obtain balanced datasets. To deal with the dataset imbalance, Synthetic Minority Over-sampling Technique (SMOTE) is utilized to generate minority samples to achieve a dataset balance. Additionally, besides conventional features, we use two types of new features, residue interface propensity previously developed by us, and topological features obtained using node-weighted networks, and propose an effective Random Grouping feature selection strategy combined with a two-step method to determine an optimal feature set. Finally, a stacking ensemble classifier is adopted to build our model. The results show SREPRHot achieves a good performance with SEN, MCC and AUC of 0.900, 0.557 and 0.829 on the independent testing dataset. The comparison study indicates SREPRHot shows a promising performance. AVAILABILITY AND IMPLEMENTATION The source code is available at https://github.com/ChunhuaLiLab/SREPRHot. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.