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Citations per year

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Protocols

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

Versioning


No version available

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This tool is not available anymore.

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 citations

 (21)
library_books

Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools

2018
Front Genet
PMCID: 5780412
PMID: 29403526
DOI: 10.3389/fgene.2017.00231

[…] The iFoldRNA web server performs automated prediction of RNA structure and analyses of thermodynamic folding. In its previous version (Sharma et al., ), only prediction of short RNA molecules (<50 nt) was […]

call_split

Computational Methods for Modeling Aptamers and Designing Riboswitches

2017
Int J Mol Sci
PMCID: 5713409
PMID: 29149090
DOI: 10.3390/ijms18112442
call_split See protocol

[…] 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 comp […]

library_books

Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide–nucleotide interactions from direct coupling analysis

2017
Nucleic Acids Res
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 nucleotide […]

library_books

Capturing RNA Folding Free Energy with Coarse Grained Molecular Dynamics Simulations

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

[…] with 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 D […]

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

[…] ed with good accuracy (RMSD < 2.5 Å), one loop has an RMSD of 3.01 Å and two have RMSDs around 6-7 Å. We compared the results with a homology modeling based predictor RLooM and an ab initio predictor iFoldRNA. It was found that RNApps performs comparably with RLooM while considerably better than iFoldRNA. However, we also noted that RLooM cannot guarantee a return of valid structures for some targ […]

library_books

Arid5a regulates naive CD4+ T cell fate through selective stabilization of Stat3 mRNA

2016
PMCID: 4821647
PMID: 27022145
DOI: 10.1084/jem.20151289

[…] nd 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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