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HiRE-RNA specifications

Information


Unique identifier OMICS_17986
Name HiRE-RNA
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 3.0
Stability Stable
Requirements
VirtualBox
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Samuela Pasquali

Publication for HiRE-RNA

HiRE-RNA citations

 (8)
library_books

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

2018
PMCID: 5920944
PMID: 29297679
DOI: 10.1021/acs.chemrev.7b00427

[…] nd hydrogen-bond interactions between bases. In addition, there is an explicit correction for the entropy of loop formation because it was found to be underestimated by this type of CG representation.HiRe-RNA− is a high-resolution CG model in which nucleotides containing purines and pyrimidines are modeled using seven and six beads, respectively: two corresponding to the phosphate group, three to […]

library_books

Capturing RNA Folding Free Energy with Coarse Grained Molecular Dynamics Simulations

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

[…] al. derives its parameters from nearest neighbor energies and experimentally determined structures. TOPRNA captures effects of secondary structure constraints on loop conformations and free energies. HiRE-RNA depicts six-seven pseudoatoms per nucleotide with five pseudoatoms along the backbone. SimRNA, Bernauer et al., as well as the previous generation and current RACER model studied, all represe […]

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

[…] rams 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, this is not a complete list due to the rapid deve […]

library_books

Physics based RNA structure prediction

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

[…] C3′, respectively. iFoldRNA (Sharma et al. ) and Vfold (Cao and Chen ; Shi et al. ) represent RNA by three pseudo-atoms per residue. Ren (Xia et al. , ) uses 5-bead to represent each nucleotide, and HiRE-RNA (Pasquali and Derreumaux ) uses six or seven pseudo-atoms for purine and pyrimidine residues, respectively. Coarse-grained systems are usually modeled with knowledge-based potentials that are […]

library_books

A unified coarse grained model of biological macromolecules based on mean field multipole–multipole interactions

2014
J Mol Model
PMCID: 4139597
PMID: 25024008
DOI: 10.1007/s00894-014-2306-5

[…] own in Fig. .Fig. 5The coarse-grained DNA model from the Ouldridge group, which uses Morse-like potentials to reproduce base pairing and stacking with base-pair-type specific parameters [, ], and the HiRe-RNA model from the Derreumaux group [, , ], which uses Gaussian-type multibody terms to account for base pairing, can also fold nucleic acid molecules. However, both of these contain more interac […]

library_books

The power of coarse graining in biomolecular simulations

2013
PMCID: 4171755
PMID: 25309628
DOI: 10.1002/wcms.1169

[…] The recent HiRE-RNA model by Pasquali and Derreumaux is a physics-based model for RNA folding, similar to the OPEP model for proteins. The model uses one bead for the phosphate, four beads for the sugar, and one […]

Citations

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HiRE-RNA institution(s)
Laboratoire de Biochimie Theorique UPR 9080 CNRS, Universite Paris Diderot, Sorbonne, Paris Cite, IBPC, Paris, France; Institut Universitaire de France, Paris, France
HiRE-RNA funding source(s)
Supported in part by the “Initiative d’Excellence” program from the French State (Grant “DYNAMO”, ANR-11-LABX-0011-01) and IUF.

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