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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

 (21)
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

[…] ranslation (Miller et al., ). Other viral genera also use long-distance base-pairing or interaction with rRNA (Deforges et al., ). Published models of two such complex structures have been made using RNA2D3D (Mccormack et al., ) and MC-Sym (Wang et al., ; Newburn and White, ). […]

library_books

Capturing RNA Folding Free Energy with Coarse Grained Molecular Dynamics Simulations

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

[…] sed 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; this impro […]

library_books

Advancement of the Emerging Field of RNA Nanotechnology

2017
ACS Nano
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
PLoS Comput Biol
PMCID: 4975501
PMID: 27494763
DOI: 10.1371/journal.pcbi.1005032

[…] urce 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

Structure Prediction: New Insights into Decrypting Long Noncoding RNAs

2016
Int J Mol Sci
PMCID: 4730372
PMID: 26805815
DOI: 10.3390/ijms17010132

[…] RNA2D3D [], different from other structure prediction methods, is based on unpaired bases derived from Assisted Model Building with Energy Refinement (AMBER) [] and canonical base-pairings of the A-fo […]

library_books

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

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

[…] towards 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 wit […]

Citations

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

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