RNAComposer protocols

View RNAComposer computational protocol

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RNAComposer specifications

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Unique identifier OMICS_04459
Name RNAComposer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for RNAComposer

RNAComposer in pipelines

 (2)
2018
PMCID: 5882922
PMID: 29615727
DOI: 10.1038/s41598-018-23845-x

[…] constraints together with nearest neighbor thermodynamic parameters using -0.8 kcal/mol and 2.6 for the intercept (b) and slope (m), respectively. these secondary structures were used as input in rnacomposer to model the 3d rna structure using default parameters. 3d structures graphics were performed with the ucsf chimera package., , gloria lozano and rosario francisco-velilla […]

2015
PMCID: 4737167
PMID: 26704983
DOI: 10.1093/nar/gkv1488

[…] () web servers, respectively. both predictions were carried out using the energy/folding parameters indicated in the text. 3d models based on mfe or co-transcriptional folding were generated using rnacomposer () and measurements/rendering were performed using pymol., complexation with lipofectamine® 2000: rna was dissolved in opti-mem at a concentration of 6 μg/ml and combined […]


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RNAComposer in publications

 (40)
PMCID: 5890266
PMID: 29632392
DOI: 10.1038/s41598-018-23997-w

[…] protein (chain a) in complex with the uuguau rna molecule (chain c) (pdb 3mdg), and validated with the verify_3d software (http://services.mbi.ucla.edu/verify_3d/). on the other hand, we used the rnacomposer online software (http://rnacomposer.cs.put.poznan.pl/) to obtain a pdb structure of the guug rna motif. then, both molecules were individually submitted to molecular dynamics (md) […]

PMCID: 5882922
PMID: 29615727
DOI: 10.1038/s41598-018-23845-x

[…] to gain information about the ires conformational changes induced by the interaction with r fraction we took advantage of the rnastructure software incorporating the shape reactivity data, and the rnacomposer server. the predicted structure of the free ires element treated with ia is depicted in fig. . upon incubation with r extract no major changes in the 3d structure of domain 2 […]

PMCID: 5934618
PMID: 29415133
DOI: 10.1093/nar/gky071

[…] fragments were analyzed in 10% acrylamide-urea gels and bands were quantified by densitometry and normalized. shape data were used as constraints to generate 2d and 3d models using the mc-fold and rnacomposer pipelines (). rnafold (vienna rna web services) was routinely used to calculate the minimal folding energy of centroid rna structures and base pair probabilities., in vitro translation […]

PMCID: 5767303
PMID: 29375504
DOI: 10.3389/fmicb.2017.02634

[…] nmia reactivity values were averaged to obtain ra values for determining the conformer a structure. combining extrapolated conformer a, b, and c nmia reactivity profiles with the folding algorithm rnacomposer (popenda et al., ) produced 3d structures for “open,” “intermediate,” and “closed” variants of the hiv-2 rre illustrated in figure ., in contrast to most chemical and enzymatic rna […]

PMCID: 5817113
PMID: 29464002
DOI: 10.7150/thno.19904

[…] as described in ., we first constructed the initial 3d structure of the rna triplexes (mrnae2f1/mirna1/mirna2) as well as their two intrinsic rna duplexes (mrnae2f1/mirna1 and mrnae2f1/mirna2) using rnacomposer web server . then, these complexes were processed as described in our previous publication and further optimized using smart minimizer protocol in biovia® discovery studio 4.5 , . […]


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RNAComposer institution(s)
Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland

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