RPpocket: An RNA-Protein Intuitive Database with RNA Pocket Topology Resources.

ABSTRACT

RNA-protein complexes regulate a variety of biological functions. Thus, it is essential to explore and visualize RNA-protein structural interaction features, especially pocket interactions. In this work, we develop an easy-to-use bioinformatics resource RPpocket. This database provides RNA-protein complex interactions based on sequence, secondary structure, and pocket topology analysis. We extracted 793 pockets from 74 non-redundant RNA-protein structures. Then, we calculated the binding- and non-binding pocket topological properties and analyzed the binding mechanism of the RNA-protein complex. The results showed that the binding pockets were more extended than the non-binding pockets. We also found that long-range forces were the main interaction for RNA-protein recognition, while short-range forces strengthened and optimized the binding. RPpocket could facilitate RNA-protein engineering for biological or medical applications.