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RNABindR specifications


Unique identifier OMICS_08222
Name RNABindR
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Publications for RNABindR

RNABindR citations


The nuclear mitotic apparatus protein NuMA controls rDNA transcription and mediates the nucleolar stress response in a p53 independent manner

Nucleic Acids Res
PMCID: 5714241
PMID: 28981686
DOI: 10.1093/nar/gkx782

[…] regions was further normalized to that at region h4., the presence of rna-interacting residues in full length numa sequence (residues 1–2101) was analyzed by the rna web-based servers bindn and rnabindr (,). both servers returned as output the input sequence with each amino acid receiving either a positive or negative symbol, denoting the particular residue as either a rna-interacting […]


A Brief Review of RNA–Protein Interaction Database Resources

Noncoding RNA
PMCID: 5832006
PMID: 29657278
DOI: 10.3390/ncrna3010006

[…] including data derived from crosslinking immunoprecipitation (clip)-seq datasets (e.g., aura [], clipz []) and some that have been developed as a predictive tool such as pridictor [], bindn+ [], rnabindr []., clipdb [] is a clip-seq database for rna–protein interactions. the version has been developed to clipdb version 2: postar [], which is a resource of post-transcriptional regulation […]


Advances in the characterization of RNA‐binding proteins

PMCID: 5113702
PMID: 27503141
DOI: 10.1002/wrna.1378

[…] rnaprob employs a smoothed pssm encoding scheme to predict rna‐binding sites on proteins and shows an accuracy of 0.89. slightly different types of physicochemical properties are combined in rnabindr, that exploits accessible surface area, sequence specific entropy, hydrophobicity, secondary structure propensities, and electrostatics. in the testing phase, rnabindr identifies interface […]


The HEX 110 Hexamerin Is a Cytoplasmic and Nucleolar Protein in the Ovaries of Apis mellifera

PLoS One
PMCID: 4783013
PMID: 26954256
DOI: 10.1371/journal.pone.0151035

[…] min/max (minimum/maximal gray value), and intden (integrated density, i.e., the product of area and mean gray value)., potential rna-binding sites were searched in the hex 110 sequence using rnabindr, bindn, pprint, svm and rnabindrplus softwares [–]. we selected the most significant motifs, and only the alignments passing a threshold of 80% were considered as significant. the cnls […]


A Large Scale Assessment of Nucleic Acids Binding Site Prediction Programs

PLoS Comput Biol
PMCID: 4683125
PMID: 26681179
DOI: 10.1371/journal.pcbi.1004639

[…] the possibility of biased prediction by the programs. finally, different criteria are measured to show different aspects of the programs. the webservers assessed include bindn[], bindn+[], rnabindr[], rnabindrplus[], dbs-pred[], dbs-pssm[], kyg[], prbr[], pprint[], dnabindprot[], protedna[], displar[], dr_bind1[], aarna[], rbscore[], rbrdetector[], dnabind[], xypan[] and rnaprosite […]


Computational Prediction of RNA Binding Proteins and Binding Sites

Int J Mol Sci
PMCID: 4661811
PMID: 26540053
DOI: 10.3390/ijms161125952

[…] [] introduced a predictor for rna-binding sites using predicted secondary structure and amino acid type, and employingan artificial neural network. subsequently, terribilini et al. [] contributed rnabindr, which is a classical method to train naive bayes (nb) classifiers to predict rna-binding sites. the rb109 dataset is listed in . wang and brown developed the bindn tool, […]

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RNABindR institution(s)
Department of Genetics, Development and Cell Biology, Bioinformatics & Computational Biology Program, Iowa State University, Ames, IA, USA

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