PRIP: A Protein-RNA Interface Predictor Based on Semantics of Sequences

Abstract

RNA–protein interactions play an indispensable role in many biological processes. Growing evidence has indicated that aberration of the RNA–protein interaction is associated with many serious human diseases. The precise and quick detection of RNA–protein interactions is crucial to finding new functions and to uncovering the mechanism of interactions. Although many methods have been presented to recognize RNA-binding sites, there is much room left for the improvement of predictive accuracy. We present a sequence semantics-based method (called PRIP) for predicting RNA-binding interfaces. The PRIP extracted semantic embedding by pre-training the Word2vec with the corpus. Extreme gradient boosting was employed to train a classifier. The PRIP obtained a SN of 0.73 over the five-fold cross validation and a SN of 0.67 over the independent test, outperforming the state-of-the-art methods. Compared with other methods, this PRIP learned the hidden relations between words in the context. The analysis of the semantics relationship implied that the semantics of some words were specific to RNA-binding interfaces. This method is helpful to explore the mechanism of RNA–protein interactions from a semantics point of view.

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“…On the contrary, the bioinformatics approaches can remedy the limitation. Hundreds of bioinformatics approaches have been developed to address a wide range of issues in the field of molecular biology [13][14][15][16][17][18], including stress response protein identification [19], RNA modification identification [20][21][22], post-translational protein modification identification [23][24][25][26][27][28], and genomic island detection [18,29,30]. However, these bioinformatics approaches rely heavily on the accumulation of the known samples and the sophisticated design of algorithms.…”