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MetaDBSite specifications

Information


Unique identifier OMICS_08397
Name MetaDBSite
Interface Web user interface
Restrictions to use None
Input data Protein sequence
Input format FASTA, Raw
Computer skills Basic
Stability Stable
Maintained No

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Publication for MetaDBSite

MetaDBSite citations

 (6)
library_books

Identification and Characterization of the Diverse Stress Responsive R2R3 RMYB Transcription Factor from Hibiscus sabdariffa L.

2017
Int J Genomics
PMCID: 5664376
PMID: 29181384
DOI: 10.1155/2017/2763259

[…] ins bind DNA. This outcome diversified the overall functional characteristics, as well as sequence homology, environmental response, and cellular localization [].Modeling and interaction studies like metaDBSite analysis further authenticate the functional interaction of RMYB domain with the nucleic acid. About >76% of predicted DNA-protein active binding residues was found within the R2R3 DNA-bind […]

library_books

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

[…] reported prediction approaches have been summarized in . Slow programs DR_bind1 and RBRDetector were only tested on part of the datasets and the results are provided in the supplementary information. metaDBSite[] shows same result as BindN and was not tested explicitly. […]

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

[…] A-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 analyze DNA-binding sites, and showed higher accuracy and sensitivity []. These studies provide diverse and useful prediction tools for prot […]

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

[…] vices 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, technique, reference and link for the methods used in the present work are listed in Supplementary Table S1. These methods used differe […]

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

[…] equence-based prediction methods of DNA-binding sites, such as DP-Bind (), DBSpred (), DBS-PSSM () and BindN () in terms of their reported accuracy, sensitivity and specificity. A very recent method, metaDBSite that integrated results from other web-servers including a few of those mentioned above can predict solely on the basis of sequence information and reports a sensitivity of 77% (). While th […]

library_books

Computational systems biology: integration of sequence, structure, network, and dynamics

2011
BMC Syst Biol
PMCID: 3121109
PMID: 21689468
DOI: 10.1186/1752-0509-5-S1-S1

[…] duce the computational complexity.Protein-DNA interactions play an important role in many fundamental biological activities such as DNA replication, transcription and repair. JingNa Si et al. present metaDBSite, a meta web server to predict DNA-binding residues for DNA-binding proteins. MetaDBSite integrates the prediction results from six available online web servers: DISIS, DNABindR, BindN, Bind […]

Citations

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MetaDBSite institution(s)
Systems Biology Division, Zhejiang-California International NanoSystems Institute, Zhejiang University, Hangzhou, China
MetaDBSite funding source(s)
Ministry of Science and Technology of China (grant No. 2008DFA11320) and EU 7th framework Marie Curie Action IRESE program (grant NO. 247097)

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