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BindN+ specifications

Information


Unique identifier OMICS_03029
Name BindN+
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publication for BindN+

BindN+ citations

 (9)
library_books

TIS7 induces transcriptional cascade of methylosome components required for muscle differentiation

2016
BMC Biol
PMCID: 5080701
PMID: 27782840
DOI: 10.1186/s12915-016-0318-6

[…] ta demonstrated the functional relevance of this minimal essential region for TIS7-mediated activation of ICln transcription. Using bioinformatics prediction software (DISIS (www.predictprotein.org), BinDN+ (http://bioinfo.ggc.org/bindn+/), DP-Bind (http://lcg.rit.albany.edu/dp-bind/), and DNABindR (http://turing.cs.iastate.edu/PredDNA/); Additional file : Figure S2) we identified, with 70–80 % pr […]

call_split

In silico selection of an aptamer to estrogen receptor alpha using computational docking employing estrogen response elements as aptamer alike molecules

2016
Sci Rep
PMCID: 4761961
PMID: 26899418
DOI: 10.1038/srep21285
call_split See protocol

[…] e taken from Protein Data Bank and prepared for dockings by deleting undesired protein chains and ligand. For AutoDock Vina, the grid box was specified in the coordinate system of ER corresponding to BindN+ predicted RNA-binding amino acids. Grid box was created with a default value of 0.375 Å for spacing between the grid points centering at 11.139, 10.861, 9.611 and 60, 62, 68 points in x, y and […]

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

[…] SSM, DBS-Pred, RBRIdent, PPRInt, PRBR, DNABind, RBRDetector and ProteDNA were used with default parameter. The DISPLAR program was provided by Sanbo Qin and was run with default parameters. BindN and BindN+ were used by default parameters, while suffix “_RNA” and “_DNA” are RNA mode and DNA mode respectively. PRNA and Predict_RBP were trained on PRNA_R205 and BindN_R107 respectively, without cross […]

library_books

Computational learning on specificity determining residue nucleotide interactions

2015
Nucleic Acids Res
PMCID: 4666365
PMID: 26527718
DOI: 10.1093/nar/gkv1134

[…] For each DBD family, we have written network scripts to send the testing DBD sequences to the BindN web-server, BindN+ web-server and DISIS web-server for obtaining their predictions with the default settings suggested. Briefly, BindN is a support vector machine classifier using physicochemical sequence feature […]

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

[…] ein-RNA complex 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%, […]

call_split

Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins

2013
Nucleic Acids Res
PMCID: 3763535
PMID: 23788679
DOI: 10.1093/nar/gkt544
call_split See protocol

[…] e available methods for predicting the binding sites in DNA-binding proteins from amino acid sequence, which have either online services or available standalone programs (). The methods are BindN (), BindN+ (), BindN-RF (), DBS-Pred (), DBS-PSSM (), DNABindR (), DP-Bind with three categories, binary, BLOSUM and PSSM encoding (), metaDBSite () and NAPS (). The details about the name, features, tech […]

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BindN+ institution(s)
Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA

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