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RNAComposer specifications

Information


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 citations

 (45)
library_books

Targeting the polyadenylation factor EhCFIm25 with RNA aptamers controls survival in Entamoeba histolytica

2018
Sci Rep
PMCID: 5890266
PMID: 29632392
DOI: 10.1038/s41598-018-23997-w

[…] m25 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) simulati […]

library_books

Ribosome dependent conformational flexibility changes and RNA dynamics of IRES domains revealed by differential SHAPE

2018
Sci Rep
PMCID: 5882922
PMID: 29615727
DOI: 10.1038/s41598-018-23845-x

[…] nge 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. […]

call_split

Translation initiation of alphavirus mRNA reveals new insights into the topology of the 48S initiation complex

2018
Nucleic Acids Res
PMCID: 5934618
PMID: 29415133
DOI: 10.1093/nar/gky071
call_split See protocol

[…] g. 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. […]

library_books

Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools

2018
Front Genet
PMCID: 5780412
PMID: 29403526
DOI: 10.3389/fgene.2017.00231

[…] RNAComposer is a server for the prediction of the 3D structure in RNA molecules of up to 500 nt (Popenda et al., ; Biesiada et al., ). The server predicts RNA structure based on the secondary structur […]

library_books

Probing the Structures of Viral RNA Regulatory Elements with SHAPE and Related Methodologies

2018
Front Microbiol
PMCID: 5767303
PMID: 29375504
DOI: 10.3389/fmicb.2017.02634

[…] 10 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 . […]

library_books

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs

2018
Front Microbiol
PMCID: 5758548
PMID: 29354101
DOI: 10.3389/fmicb.2017.02582

[…] aki et al., ; Table , Figure ).RNA 3D structures can also be predicted directly from sequences. The accuracy of these prediction tools has improved in the past few years (Miao and Westhof, ), such as RNAComposer (Popenda et al., ; Antczak et al., ), 3dRNA (Zhao et al., ; Wang et al., ) and SimRNAweb (Magnus et al., ). Notably, SimRNAweb has accurately predicted a previously solved frameshifting RN […]

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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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