RBPBind: Quantitative prediction of Protein-RNA Interactions

TL;DR

RBPBind is a web-based tool that predicts RNA-protein interactions quantitatively, including binding curves and probabilities, by integrating RNA secondary structure effects using modified Vienna RNA package code.

Contribution

It introduces a novel web server that accurately models RNA secondary structure effects on protein binding, providing detailed quantitative predictions.

Findings

Accurately predicts binding curves and constants.

Incorporates RNA secondary structure effects.

Provides probability of binding at nucleotide level.

Abstract

Summary: We introduce RBPBind, a web-based tool for the quantitative prediction of RNA-protein interactions. Given a user-specified RNA and a protein selected from a set of several common RNA-binding proteins, RBPBind computes the binding curve and effective binding constant of the reaction in question. The server also computes the probability that, at a given concentration of protein, a protein molecule will bind to any particular nucleotide along the RNA. The software for RBPBind is adapted from the Vienna RNA package, whose source code has been modified to accommodate the effects of single stranded RNA binding proteins. RBPBind thus fully incorporates the effect of RNA secondary structure on protein-RNA interactions. Availability: Our web server is available at http://bioserv.mps.ohio-state.edu/RBPBind