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BindN specifications

Information


Unique identifier OMICS_08389
Name BindN
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence.
Input format FASTA
Computer skills Basic
Stability No
Maintained No

Maintainer


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Publication for BindN

BindN citations

 (26)
library_books

Biochemical characterization of INTS3 and C9ORF80, two subunits of hNABP1/2 heterotrimeric complex in nucleic acid binding

2018
PMCID: 5748837
PMID: 29150435
DOI: 10.1042/BCJ20170351

[…] e N-terminal region of INTS3 does not bind with ssDNA []; however, in our present study, we found that the INTS3FL bound ssRNA and ssDNA. Hence, we predicted the DNA-binding residues of INTS3FL using BindN [] with 90% of expected specificity. The results suggested that the C-terminal region has more positive predictions for DNA binding (Supplementary Figure S6). To evaluate this, we divided the IN […]

library_books

A putative RNA binding protein from Plasmodium vivax apicoplast

2017
FEBS Open Bio
PMCID: 5794462
PMID: 29435408
DOI: 10.1002/2211-5463.12351

[…] g β2 and the C‐terminal α3‐helix; and also with the finding that a higher salt concentration in the buffer disrupted the binding of apiRBP to target U‐rich RNAs by ITC. Finally, the prediction server BindN localized potential RNA binding sites that were out of the limits of the strands β1 and β3 (particularly concentrated in β2). Then, if RNA recognition was β2‐mediated, this highly dynamic secon […]

library_books

Molecular characterization of emaraviruses associated with Pigeonpea sterility mosaic disease

2017
Sci Rep
PMCID: 5605523
PMID: 28928453
DOI: 10.1038/s41598-017-11958-8

[…] of conserved amino acid sequence motifs, NVLSFNK134–140, NRLA183–186 and GYEF204–207 with the other viruses of the genus Emaravirus as reported,, predicted to be associated with RNA-binding (Table ). BindN analysis of NC protein of PPSMVs predicted stretch amino acid sequences at N′-terminal and C′-terminal regions also predicted to play a possible role in RNA binding. In the present study, we det […]

library_books

The identification of FANCD2 DNA binding domains reveals nuclear localization sequences

2017
Nucleic Acids Res
PMCID: 5737651
PMID: 28666371
DOI: 10.1093/nar/gkx543

[…] s 65–84 indicated with a green box) lead to intense DNA binding (Figure ). A minor signal was detected in peptide 4 (amino acids 49–68). The bioinformatic analysis by DNA binding prediction algorithm BindN (http://bioinfo.ggc.org/bindn/) predicted a few DNA binding residues in F1C with high scores (Figure ). The sequences corresponding to the peptide 2 (red letters Figure ), and 5 (green letters F […]

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 tool (htt […]

library_books

Structural elucidation of a novel mechanism for the bacteriophage based inhibition of the RNA degradosome

2016
eLife
PMCID: 4980113
PMID: 27447594
DOI: 10.7554/eLife.16413.031

[…] Figure 2—figure supplement 1.Bioinformatic analyses of the second Dip binding fragment of RNase E (residues 756–835) suggested that this region may encompass an RNA binding motif at residues 757–772 (BindN; ) and a possible protein binding site at residues 776–835 (ANCHOR). In , only a clear shift of Dip is visible upon addition of the RNase E fragments harbouring the predicted RNA binding site of […]

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BindN institution(s)
Bioinformatics Center, Division of Biology, Kansas State University Manhattan, KS, USA
BindN funding source(s)
This work was supported by the K-INBRE Bioinformatics Core (NIH grant number P20 RR016475).

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