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RNABindR specifications

Information


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

 (8)
call_split

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

2016
PLoS One
PMCID: 4783013
PMID: 26954256
DOI: 10.1371/journal.pone.0151035
call_split See protocol

[…] 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 Mapper […]

call_split

A Large Scale Assessment of Nucleic Acids Binding Site Prediction Programs

2015
PLoS Comput Biol
PMCID: 4683125
PMID: 26681179
DOI: 10.1371/journal.pcbi.1004639
call_split See protocol

[…] Li lab and Xiaoyong Pan provided RNAProSite and xypan prediction results respectively, with default parameter. aaRNA was used by inputting the structure file with default parameters. RNABindR and RNABindRPlus were predicted with default parameters, while removing 95% sequence identity in RNABindRPlus. KYG was predicted with command line using “method_type = 8” option. RBscore_SVM […]

library_books

Prediction of RNA Binding Residues: An Extensive Analysis Based on Structure and Function to Select the Best Predictor

2014
PLoS One
PMCID: 3962366
PMID: 24658593
DOI: 10.1371/journal.pone.0091140

[…] plex structures (since June 2012). The prediction results of each method in these two datasets were presented in the . The accuracy of all the methods in both datasets lies between 55–71%. BindN+ and RNABindR v2.0 showed the best performance in both datasets at the distance cutoff of ≤3.5 Å and ≤6.0 Å, respectively. Pprint and NAPS performed well with an average accuracy of 66% and 61%, respective […]

library_books

Prediction of RNA binding amino acids from protein and RNA sequences

2011
BMC Bioinformatics
PMCID: 3278847
PMID: 22373313
DOI: 10.1186/1471-2105-12-S13-S7

[…] dues in protein sequences. For example, BindN [] uses a support vector machine (SVM) to predict the RNA- or DNA-binding residues in a protein sequence based on the chemical properties of amino acids. RNABindR [,] predicts the RNA-binding residues in a protein sequence using a Naïve Bayes classifier. However, none of these consider interacting partners (i.e., RNA) for a given protein when predictin […]

library_books

Predicting RNA binding residues from evolutionary information and sequence conservation

2010
BMC Genomics
PMCID: 3005934
PMID: 21143803
DOI: 10.1186/1471-2164-11-S4-S2

[…] alignment. Terribilini et al. (2006) [] applied a Naïve Bayes classifier with amino acid sequence information for predicting RNA interacting residues and presented the results through the web service RNABindR []. The ability to computationally predict RNA-binding residues in a RNA-binding protein can help biologists reveal site-directed mutagenesis in wet-lab experiments.Caragea et al. [] explored […]

call_split

UPF201 Archaeal Specific Family Members Reveal Structural Similarity to RNA Binding Proteins but Low Likelihood for RNA Binding Function

2008
PLoS One
PMCID: 2596488
PMID: 19079550
DOI: 10.1371/journal.pone.0003903
call_split See protocol

[…] 3D (http://sunserver.cdfd.org.in:8080/protease/PAR_3D/access.html) was used, though none was identified . 6) Putative RNA binding residues were identified using BindN (http://bioinfo.ggc.org/bindn/), RNAbindR (http://bindr.gdcb.iastate.edu/RNABindR/), and KYG (http://yayoi.kansai.jaea.go.jp/qbg/kyg/index.php) –. 7) Conserved residues were mapped onto the structure using ConSurf . 8) For phylogenet […]

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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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