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Protocols

DISPLAR specifications

Information


Unique identifier OMICS_08398
Name DISPLAR
Interface Web user interface
Restrictions to use None
Input data Protein structures in PDB format
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Huan-Xiang Zhou

Publication for DISPLAR

DISPLAR citations

 (11)
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

[…] using “method_type = 8” option. RBscore_SVM was based on the training set of R246. DBS-PSSM, 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. […]

library_books

Computational learning on specificity determining residue nucleotide interactions

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

[…] can be compared to the structural methods for model testing. Thus we have also written network scripts to send the structural information of each testing DBD sequence to the DBD-Hunter web-server and DISPLAR web-server with the default settings suggested. Briefly, DBD-Hunter is a structural template matching method using statistical potential () while DISPLAR is a neural network method taking into […]

library_books

DNA barcodes from four loci provide poor resolution of taxonomic groups in the genus Crataegus

2015
PMCID: 4480070
PMID: 25926325
DOI: 10.1093/aobpla/plv045

[…] a, clade A1). However, an equally distinct cluster (Supporting Information—Fig. S2, clade C2) comprises all three individuals of diploid C. marshallii (series Apiifoliae in section Crataegus) plus C. displar, a tetraploid in series Lacrimatae (section Coccineae). Another example is C. pinnatifida (section Crataegus); ITS2 sequences were obtained for two of the individuals of this species [see Supp […]

library_books

An Overview of the Prediction of Protein DNA Binding Sites

2015
Int J Mol Sci
PMCID: 4394471
PMID: 25756377
DOI: 10.3390/ijms16035194

[…] s, meta-prediction [] and comparative study work [] is required. These methods are robust and effective in many applications, including DNA-binding site prediction. For example, the prediction method DISPLAR was constructed using two-layer neural networks [], and SeqPredNet was constructed using a delicate three-layered network []. The metaDBSite integrated six online Web servers to predict and an […]

library_books

A graph kernel method for DNA binding site prediction

2014
BMC Syst Biol
PMCID: 4290685
PMID: 25521807
DOI: 10.1186/1752-0509-8-S4-S10

[…] ck of a standardized benchmark for the evaluation. Here, it is not our intent to make a systematic comparison between different methods. We only compared our method with two recent methods, MV [] and DISPLAR [], regarding their ability to find DNA-binding sites on the 13 unbound proteins. Both MV and DISPLAR use both structural and sequence information in predicting DNA-binding sites.The MV method […]

library_books

Characterization and prediction of the binding site in DNA binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters

2012
Nucleic Acids Res
PMCID: 3424558
PMID: 22641851
DOI: 10.1093/nar/gks405

[…] g region in the unbound form of the protein is a challenging task. Almost all earlier investigations exploited the bound complex in characterizing and identifying the DNA-binding site. A method named DISPLAR () used 14 unbound DBPs in testing and gave an accuracy of 77%. In this work we too started with the complex form in characterizing the binding site with different set of parameters, but teste […]

Citations

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DISPLAR institution(s)
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, FL, USA
DISPLAR funding source(s)
This work was supported in part by NIH grant GM58187.

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