Prediction of microRNA-binding residues in protein using a Laplacian support vector machine based on sequence...

The identification of microRNA (miRNA)-binding protein residues significantly impacts several research areas, including gene regulation and expression. We propose a method, PmiRBR, which combines a novel hybrid feature with the Laplacian support vector machine (LapSVM) algorithm to predict miRNA-binding residues in protein sequences. The hybrid feature is constituted by secondary structure, conservation scores, and a novel feature, which includes evolutionary information combined with the physicochemical properties of amino acids. Performance comparisons of the various features indicate that our novel feature contributes the most to prediction improvement. Our results demonstrate that PmiRBR can achieve 85.96% overall accuracy, with 43.89% sensitivity and 90.56% specificity. PmiRBR significantly outperforms other approaches at miRNA-binding residue prediction.