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DNAbinder specifications

Information


Unique identifier OMICS_11967
Name DNAbinder
Interface Web user interface
Restrictions to use None
Input data Protein sequences
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


Publication for DNAbinder

DNAbinder citations

 (17)
library_books

Protein Sequence Comparison and DNA binding Protein Identification with Generalized PseAAC and Graphical Representation

2018
PMCID: 5930480
PMID: 29380690
DOI: 10.2174/1386207321666180130100838

[…] 00% and 86.07%, respectively (see Table ). This demonstrates that our SVM model performs equally well on independent dataset. For convenience of comparison, results of some existing methods including DNAbinder [], DNA-Prot [], iDNA-Prot [] and enDNA-Prot [] are also listed in Table . DNAbinder developed by Kumar et al. [] can extract evolutionary information in form of position specific scoring ma […]

library_books

HMMBinder: DNA Binding Protein Prediction Using HMM Profile Based Features

2017
Biomed Res Int
PMCID: 5706079
PMID: 29270430
DOI: 10.1155/2017/4590609

[…] We have compared the performance of HMMBinder with several previous methods and tools used for DNA-binding protein prediction on the benchmark dataset benchmark1075. They are DNABinder [], DNA-Prot [], iDNA-Prot [], iDNA-Prot|dis [], DBPPred [], iDNAPro-PseAAC [], PseDNA-Pro [], Kmer1 + ACC [], and Local-DPP []. The results reported in this paper for these methods are take […]

library_books

iDNAProt ES: Identification of DNA binding Proteins Using Evolutionary and Structural Features

2017
Sci Rep
PMCID: 5668250
PMID: 29097781
DOI: 10.1038/s41598-017-14945-1

[…] t|dis, DBPPred, iDNAPro-PseAAC, PseDNA-Pro, Kmer1 + ACC, Local-DPP, etc. Kumar et al. used evolutionary information from PSSM profiles with support vector machines and established a web-server called DNABinder. They compared the effectiveness of the PSSM based features with amino acid composition, di-peptide composition and 4-parts amino acid compositions as features.DNA-Prot is another software p […]

library_books

A Small Wolbachia Protein Directly Represses Phage Lytic Cycle Genes in “Candidatus Liberibacter asiaticus” within Psyllids

2017
PMCID: 5463029
PMID: 28608866
DOI: 10.1128/mSphereDirect.00171-17

[…] ein hits had significantly fewer unique spectra and lower coverage. The Wolbachia protein also satisfied the required search criteria: (i) small size (6.65 kDa); (ii) predicted DNA binding potential (DNAbinder) (); (iii) predicted to be secreted (SecretomeP 2.0) (); (iv) extracellular (PSLpred) (). The 56-amino-acid (aa) putative repressor protein was encoded by WDIAC_RS0101550 annotated on Contig […]

library_books

DNABP: Identification of DNA Binding Proteins Based on Feature Selection Using a Random Forest and Predicting Binding Residues

2016
PLoS One
PMCID: 5132331
PMID: 27907159
DOI: 10.1371/journal.pone.0167345

[…] NA-Prot [], were proposed recently and provide web servers to predict DNA-binding proteins. These three methods all showed better performances when compared with previous methods such as DNA-Prot [], DNAbinder or iDNA-Port []. The predictor enDNA-Prot (http://bioinformatics.hitsz.edu.cn/Ensemble-DNA-Prot/) identifies DNA-binding proteins using physicochemical properties as input features and emplo […]

library_books

De novo protein function prediction using DNA binding and RNA binding proteins as a test case

2016
Nat Commun
PMCID: 5121330
PMID: 27869118
DOI: 10.1038/ncomms13424

[…] To allow for a more detailed comparison of precision-recall curves, we focused on methods that give numerical scores rather than binary classification. We submitted our own set of DBPs to DNABIND and DNAbinder. The PRC is shown in . Dr PIP performance on the non-redundant dataset significantly exceeds the other methods. […]

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DNAbinder institution(s)
Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, India; Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo, Japan

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