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Background <p>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.</p> Results <p>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.</p> Conclusions <p>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 <a href="http://www.csbio.sjtu.edu.cn/bioinf/RBPsuite/">http://www.csbio.sjtu.edu.cn/bioinf/RBPsuite/</a>.</p>

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RBPsuite 2.0: an updated RNA-protein binding site prediction suite with high coverage on species and proteins based on deep learning

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年3月11日

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  • Xiaoyong Pan,
  • Yi Fang,
  • Xiaojian Liu,
  • Xiaoyu Guo,
  • Hong-Bin Shen

摘要

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/.