Kinefold protocols

View Kinefold computational protocol

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Kinefold specifications

Information


Unique identifier OMICS_03593
Name Kinefold
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Hervé Isambert <>

Publication for Kinefold

Kinefold in pipeline

2014
PMCID: 4263765
PMID: 25503469
DOI: 10.1371/journal.ppat.1004553

[…] were predicted by the circular version of the mfold program . the obtained secondary structures were further edited for print by rnaviz 2 . to search for possible kissing-loops in ahvd-like rna, the kinefold web server was used with default parameters., we are grateful to professor francesco di serio for his help with the figures and his valuable comments, and to ricardo flores for his valuable […]


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Kinefold in publications

 (26)
PMCID: 5928113
PMID: 29712996
DOI: 10.1038/s41598-018-25273-3

[…] citrate-saturated phenol:chloroform:isoamyl alcohol (125:24:1, ph 4.7), followed by chloroform:isoamyl alcohol (24:1) and then precipitated using sodium acetate/ethanol. ∆g was obtained using http://kinefold.curie.fr/., to obtain short uncapped rnas (64 nt) for mst or emsa, the prl renilla luciferase reporter vector containing the ssa1 5′utr (40 nt) was linearized with ncoi to produce a “run […]

PMCID: 5713409
PMID: 29149090
DOI: 10.3390/ijms18112442

[…] sampling, can be used to study the large scale conformational fluctuations of rnas., also based on the coarse-grained structural model, a number of computational methods, such as rnakinetics [], kinefold [], and cofold [] are developed to simulate co-transcriptional folding pathways of mrnas from the early 1980s when key experiments show that structure formation happens co-transcriptionally […]

PMCID: 5591547
PMID: 28886711
DOI: 10.1186/s12931-017-0648-0

[…] correction via false discovery rate (fdr) estimation and significant level at 0.05 (https://genetrail2.bioinf.uni-sb.de/) []. in addition, mfold rnafold (http://unafold.rna.albany.edu/?q=mfold) and kinefold web-servers (http://kinefold.curie.fr/) were conducted to predict the secondary structures of rna sequence in a and g alleles., a total of 211 asthmatic patients and 300 controls (age range […]

PMCID: 5621056
PMID: 28867802
DOI: 10.3390/s17091990

[…] individual parts is in a way uncertain from the publication itself. however the key feature of the design process is the simulation of co-transcriptional folding of individual candidates using the kinefold web service []. in an iterative approach the authors changed sub-sequences if unwanted structural intermediates occurred in the nascent rna transcript until the simulation showed […]

PMCID: 5575007
PMID: 28852099
DOI: 10.1038/s41598-017-10085-8

[…] refined arn pattern was then used to annotate (arn)x motifs in 67 srnas. overlapping matches were merged into a single (arn)x region (table )., secondary structure predictions were performed using kinefold, mfold, and rnafold–, where (arn)x motifs were protected from base-pairing. plots were generated with mfold and colour-coding was added manually. for identifying complementary regions […]


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Kinefold institution(s)
Laboratoire de Dynamique des Fluides Complexes, CNRS-ULP, Institut de Physique, Strasbourg, France

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