iFoldRNA statistics

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iFoldRNA specifications

Information


Unique identifier OMICS_04466
Name iFoldRNA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability No
Maintained No

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Information


Unique identifier OMICS_04466
Name iFoldRNA
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publications for iFoldRNA

iFoldRNA in publications

 (16)
PMCID: 5713409
PMID: 29149090
DOI: 10.3390/ijms18112442

[…] sequences and base pairing as inputs to generate structures, and then applies replica exchange simulations with the potential to find a representative structure. based on this method, the web server ifoldrna was created for prediction of rna 3d structure []., the 3d structures of aptamers modeled by these approaches suggest that the aptamer domains often form a compact structure involving many […]

PMCID: 5499770
PMID: 28482022
DOI: 10.1093/nar/gkx386

[…] and θ (between atoms pn, c4΄n, pn+1 and c4΄n+1) are sufficient to describe rna backbone conformation in most cases (), p and c4΄ are frequently used to construct coarse-grained model, e.g. vfold (), ifoldrna (,) and simrna (,). c1΄ atom is the joint of the sugar ring and the base. we use this atom for two reasons: first, it is used as the pivot to rotate the base of a randomly selected […]

PMCID: 5385882
PMID: 28393861
DOI: 10.1038/srep45812

[…] one pseudoatom per nucleotide include yammp/yup, an adaptable user input required model, and nast, which assumes ideal helices from secondary structure and uses md and clustering to build loops. ifoldrna, denesyuk et al., and toprna use three pseudoatoms per nucleotide to depict phosphate, sugar, and nucleobase groups. ifoldrna uses discrete molecular dynamics and replica exchange molecular […]

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

[…] 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, […]

PMCID: 4821647
PMID: 27022145
DOI: 10.1084/jem.20151289

[…] spanner () with mrf-2 (protein data bank identifier 1ig6; sequence identity was 75%) as a template. stem-loops in the stat3 3′utr were identified using rna rnastructure () and rendered in 3d using ifoldrna program (; ). protein-rna docking was performed using surfit server. to consider the flexibility of the rna structure, we ran 10 × 10 ns md simulations using gromacs () with the amber ff12sb […]


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iFoldRNA institution(s)
Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, NC, USA

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