RBPsuite 2.0: an Updated RNA-protein Binding Site Prediction Suite with High Coverage on Species and Proteins Based on Deep Learning

Overview

Journal BMC Biol

Publisher Biomed Central

Specialty Biology

Date 2025 Mar 12

PMID 40069726

Authors

Xiaoyong Pan

Yi Fang

Xiaojian Liu

Xiaoyu Guo

Hong-Bin Shen

Affiliations

Soon will be listed here.

Abstract

Background: RNA-binding proteins (RBPs) play crucial roles in many biological processes, and computationally identifying RNA-RBP interactions provides insights into the biological mechanism of diseases associated with RBPs.

Results: To make the RBP-specific deep learning-based RBP binding sites prediction methods easily accessible, we developed an updated easy-to-use webserver, RBPsuite 2.0, with an updated web interface for predicting RBP binding sites from linear and circular RNA sequences. RBPsuite 2.0 has a higher coverage on the number of supported RBPs and species compared to the original RBPsuite, supporting an increased number of RBPs from 154 to 353 and expanding the supported species from one to seven. Additionally, RBPsuite 2.0 replaces the CRIP built into RBPsuite 1.0 with iDeepC, a more accurate RBP binding site predictor for circular RNAs. Furthermore, RBPsuite 2.0 estimates the contribution score of individual nucleotides on the input sequences as potential binding motifs and links to the UCSC browser track for better visualization of the prediction results.

Conclusions: RBPsuite 2.0 is an updated, more comprehensive webserver for predicting RBP binding sites in both linear and circular RNA sequences. It supports more RBPs and species and provides more accurate predictions for circular RNAs. The tool is freely available at http://www.csbio.sjtu.edu.cn/bioinf/RBPsuite/ .

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