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Protocols

CentroidFold specifications

Information


Unique identifier OMICS_03449
Name CentroidFold
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for CentroidFold

CentroidFold citations

 (32)
call_split

Capturing alternative secondary structures of RNA by decomposition of base pairing probabilities

2018
BMC Bioinformatics
PMCID: 5836843
PMID: 29504917
DOI: 10.1186/s12859-018-2018-4
call_split See protocol

[…] In the proposed method, the reference secondary structure is the structure estimated by CentroidFold []. Alternatively, of course, any reliable prediction by another tool, such as the minimum free energy structure by Mfold [] can be used. […]

library_books

Effects of mRNA secondary structure on the expression of HEV ORF2 proteins in Escherichia coli

2017
Microb Cell Fact
PMCID: 5686824
PMID: 29137642
DOI: 10.1186/s12934-017-0812-8

[…] The secondary structures of the mRNA were predicted by the CentroidFold algorithm and are shown in Additional file : Figure S1. The mRNA secondary structures of the non-expressed genes were more stable than the ones of the expressed genes, with the free energ […]

library_books

An RNA editing/dsRNA binding independent gene regulatory mechanism of ADARs and its clinical implication in cancer

2017
Nucleic Acids Res
PMCID: 5737565
PMID: 28985428
DOI: 10.1093/nar/gkx667

[…] double stranded RNA (dsRNA) structure is essential for ADARs binding and A-to-I RNA editing (), 3′UTR sequences of both METTL7A and RBBP9 were predicted to form long dsRNA secondary structures using CentroidFold () (). As expected, in HEK293T cells transfected with increasing amounts of either ADAR1 or ADAR2 expression construct, a dose-dependent reduction in luciferase activity of pmirGLO-METTL7 […]

library_books

Synthetic mRNA devices that detect endogenous proteins and distinguish mammalian cells

2017
Nucleic Acids Res
PMCID: 5499560
PMID: 28525643
DOI: 10.1093/nar/gkx298

[…] nslation in the presence of the trigger plasmid (∼30% repression) (Figure ). We speculated that the U1utr forms a less-stabilized secondary structure that may affect the U1A–mRNA interaction, because CentroidFold software () predicted that U1utr did not form the expected secondary structure reported previously () (). Thus, we replaced nucleotides of U1utr and newly designed the U1utr_stb aptamer t […]

library_books

Identification of protein structural elements responsible for the diversity of sequence preferences among Mini III RNases

2016
Sci Rep
PMCID: 5141509
PMID: 27924926
DOI: 10.1038/srep38612

[…] otide long sequences flanking in the alignment the position of the known 5′ and 3′ BsMiniIII cleavage sites in B. subtilis 23 S pre-rRNA were extracted and used in secondary structure prediction with CentroidFold web server using default parameters. Secondary structure prediction was carried out using PSIPRED using default parameters. […]

call_split

In Silico Design of a Chimeric Protein Containing Antigenic Fragments of Helicobacter pylori; A Bioinformatic Approach

2016
PMCID: 4899534
PMID: 27335622
DOI: 10.2174/1874285801610010097
call_split See protocol

[…] her by the Mfold Web-based software (mfold.rna.albany.edu) [], the RNAfold online server (rna.tbi.univie.ac.at) and GeneBee (www.genebee.msu.su/services/ rna2_reduced.html). Results were confirmed by CentroidFold Web Server, indicated the mRNA was stable enough for effectual translation in the prokaryotic host []. […]


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CentroidFold institution(s)
Japan Biological Informatics Consortium, Koto-ku, Tokyo, Japan

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