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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

 (7)
library_books

Ten simple rules to create a serious game, illustrated with examples from structural biology

2018
PMCID: 5843163
PMID: 29518072
DOI: 10.1371/journal.pcbi.1005955

[…] scientific data. it is possible to build a set of rules providing a guideline to create or improve serious games. we present arguments gathered from our own experience (phylo, docmolecules, the hire-rna contest and pangu) as well as examples from the growing literature on scientific serious games., science has an enormous impact on society; therefore, understanding and participating […]

library_books

Capturing RNA Folding Free Energy with Coarse Grained Molecular Dynamics Simulations

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

[…] 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, […]

library_books

Structure Prediction of RNA Loops with a Probabilistic Approach

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

[…] 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 […]

library_books

Physics based RNA structure prediction

2015
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 […]

library_books

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

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

[…] in fig. .fig. 5, the 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 […]

library_books

The power of coarse graining in biomolecular simulations

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

[…] qualitatively effects such as experimentally observed narrowing of the minor groove due to cations, but the increased detail rendered it roughly 30% slower than the implicit model., 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, […]


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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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