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RNA2D3D specifications

Information


Unique identifier OMICS_10684
Name RNA2D3D
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Bruce Shapiro <>

Publication for RNA2D3D

RNA2D3D citations

 (16)
library_books

Capturing RNA Folding Free Energy with Coarse Grained Molecular Dynamics Simulations

2017
PMCID: 5385882
PMID: 28393861
DOI: 10.1038/srep45812

[…] models include the mc-fold/mc-sym pipeline, barnacle, rsim, 3drna, rnacomposer, vfold, rna-moip and farna/farfar available in the rosetta package. similar to template based modeling, assemble and rna2d3d use homologous rna structures to predict the new rna structure (with manual refinement available). in graph theory techniques, rna is depicted topologically to build rna structures; […]

library_books

Advancement of the Emerging Field of RNA Nanotechnology

2017
PMCID: 5333189
PMID: 28045501
DOI: 10.1021/acsnano.6b05737

[…] nanoprisms designed from prna (b-ii).,,,,− (6) construction of rna nanoparticles via computational design. several software programs have been developed over the years, such as nanotiler, assemble2, rna2d3d, info-rna, and nupack, which are useful to design de novo rna nanoparticles. examples are a six-membered rna nanoring and an rna nanocube generated using nanotiler (c). long sequences as well […]

library_books

Structure Prediction of RNA Loops with a Probabilistic Approach

2016
PMCID: 4975501
PMID: 27494763
DOI: 10.1371/journal.pcbi.1005032

[…] of gaining structural information. many programs have been developed to assist rna 3d structure prediction, including yammp [], nab [], erna-3d [], manip [], s2s [], farna [], mc-fold/mc-sym [], rna2d3d [], ifoldrna [, ], nast [], assemble [], hire-rna [], farfar [], rnabuilder [], moderna [], oxrna [], 3drna [], a coarse-grained model that includes salt effect [], our pk3d [], etc. however, […]

library_books

RNA 3D Modules in Genome Wide Predictions of RNA 2D Structure

2015
PMCID: 4624896
PMID: 26509713
DOI: 10.1371/journal.pone.0139900

[…] functional relevancy., although more recent development has shown progress with regard to combining 2d and 3d structure prediction, none seem feasible at a genome-wide level. approaches such as rna2d3d [] and assemble [] are semi-automated where the user is in charge of modifying a given secondary structure by adding 3d modules or editing the backbone torsion angles. combining 3d modules […]

library_books

RNA as a stable polymer to build controllable and defined nanostructures for material and biomedical applications

2015
PMCID: 4707685
PMID: 26770259
DOI: 10.1016/j.nantod.2015.09.003

[…] program developed by zuker 30 years ago []. it is expected that computer algorithms will facilitate rna nanoparticle construction. a variety of computer programs such as nanofolder, nanotiler and rna2d3d are available to facilitate the in silico design of rna sequences (these sequences may contain inter-strand and intra-strand pseudoknot-like interactions) capable of self-assembly […]

library_books

Physics based RNA structure prediction

2015
PMCID: 4762127
PMID: 26942214
DOI: 10.1007/s41048-015-0001-4

[…] for small rnas (<50 nt). however, the method is mostly limited to short rnas because of the rapid increase in complexity of the probabilistic model., many rna structure design algorithms, such as rna2d3d (martinez et al. ) and assemble (jossinet et al. ), are quite efficient. this interactive graphical tools are useful to analyze and build rna architectures, but have less ability for rna […]


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RNA2D3D institution(s)
Center for Cancer Research, Nanobiology Program, National Cancer Institute, Frederick, MD, USA

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