PRA-Pred Protein-RNA complex Binding Affinity Prediction

About PRA-Pred

Binding affinity prediction of protein-RNA complexes

Protein-RNA interactions play a major role in several cellular and biological processes. Elucidating the factors influencing the binding affinity of protein-RNA complexes and predicting their free energy of binding provide deep insights for understanding the recognition mechanism.

Results

In this work, we have collected the experimental binding affinity data for a set 217 protein-RNA complexes and derived several structure-based features such as contact potentials, interaction energy and contacts between different types of atoms, RNA base step parameters.Our analysis on relationship between binding affinity and structural features revealed that the important factors depend on the number of RNA strands, and functional and structural classes of proteins. Generally, RNA base step parameters, interactions between various atoms, hydrogen bonds and energy contributions are important to understand the binding affinity. Further, we have developed multiple regression equations for predicting the binding affinity of protein-RNA complexes belonging to different structural and functional classes of protein-RNA complexes.Our method showed an average correlation and mean absolute error of 0.77 and 1.02, respectively between experimental and predicted binding affinities on a jack-knife test.

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