RBPsuite: RNA-protein Binding Sites Prediction Suite Based on Deep Learning

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2020 Dec 10

PMID 33297946

Citations 34

Authors

Xiaoyong Pan

Yi Fang

Xianfeng Li

Yang Yang

Hong-Bin Shen

Affiliations

Soon will be listed here.

Abstract

Background: RNA-binding proteins (RBPs) play crucial roles in various biological processes. Deep learning-based methods have been demonstrated powerful on predicting RBP sites on RNAs. However, the training of deep learning models is very time-intensive and computationally intensive.

Results: Here we present a deep learning-based RBPsuite, an easy-to-use webserver for predicting RBP binding sites on linear and circular RNAs. For linear RNAs, RBPsuite predicts the RBP binding scores with them using our updated iDeepS. For circular RNAs (circRNAs), RBPsuite predicts the RBP binding scores with them using our developed CRIP. RBPsuite first breaks the input RNA sequence into segments of 101 nucleotides and scores the interaction between the segments and the RBPs. RBPsuite further detects the verified motifs on the binding segments gives the binding scores distribution along the full-length sequence.

Conclusions: RBPsuite is an easy-to-use online webserver for predicting RBP binding sites and freely available at http://www.csbio.sjtu.edu.cn/bioinf/RBPsuite/ .

Citing Articles

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

Pan X, Fang Y, Liu X, Guo X, Shen H BMC Biol. 2025; 23(1):74.

PMID: 40069726 PMC: 11899677. DOI: 10.1186/s12915-025-02182-2.

RBPMS inhibits bladder cancer metastasis by downregulating MYC pathway through alternative splicing of ANKRD10.

Yu J, Chen L, Wang G, Qian K, Weng H, Yang Z Commun Biol. 2025; 8(1):367.

PMID: 40044952 PMC: 11882939. DOI: 10.1038/s42003-025-07842-1.

NONO regulates mC modification and alternative splicing of PTEN mRNAs to drive gastric cancer progression.

Zhao G, Liu R, Ge L, Qi D, Wu Q, Lin Z J Exp Clin Cancer Res. 2025; 44(1):81.

PMID: 40033337 PMC: 11877715. DOI: 10.1186/s13046-024-03260-z.

EnrichRBP: an automated and interpretable computational platform for predicting and analysing RNA-binding protein events.

Wang Y, Zhu H, Wang Y, Yang Y, Huang Y, Zhang J Bioinformatics. 2025; 41(1).

PMID: 39804669 PMC: 11783304. DOI: 10.1093/bioinformatics/btaf018.

DeepMiRBP: a hybrid model for predicting microRNA-protein interactions based on transfer learning and cosine similarity.

Azizian S, Cui J BMC Bioinformatics. 2024; 25(1):381.

PMID: 39695955 PMC: 11656930. DOI: 10.1186/s12859-024-05985-2.

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