RBPBind: Quantitative prediction of Protein-RNA Interactions

2016/11/04 by Jeff Gaither, Yi‐Hsuan Lin, Yi-Hsuan Lin +4
Biochemistry, Genetics and Molecular Biology · #Biomolecules (q-bio.BM) #FOS: Biological sciences #RNA Research and Splicing #RNA and protein synthesis mechanisms #RNA modifications and cancer #q-bio.BM

paper · pdf · doi:10.48550/arxiv.1611.01245

arxiv created 2016/11/04 · openalex publication_date 2016/11/04 · arxiv updated 2016/11/07 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

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

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