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Citations per year

Number of citations per year for the bioinformatics software tool Vfold
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Tool usage distribution map

This map represents all the scientific publications referring to Vfold per scientific context
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Vfold specifications

Information


Unique identifier OMICS_11620
Name Vfold
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Shi-Jie Chen

Information


Unique identifier OMICS_11620
Name Vfold
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Shi-Jie Chen

Publication for Vfold

Vfold citations

 (16)
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 Vfold model (Cao and Chen, ) is based on a multi-scaling strategy to predict RNA free energy landscapes and 3D structures based on an input sequence. The secondary structure is predicted from the nucl […]

library_books

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

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

[…] possibly the salt dependency of the stability of hairpins, duplexes, and pseudoknots, among other types of RNA structures. In some cases, certain mechanical properties have been reported as well.The Vfold model proposed by Cao and Chen, uses an estimate of the free energy based on NN parameters. It decomposes a secondary structure into arrays of stacked pairs and unstacked loops. The free energy […]

library_books

Theory Meets Experiment: Metal Ion Effects in HCV Genomic RNA Kissing Complex Formation

2017
Front Mol Biosci
PMCID: 5744182
PMID: 29312955
DOI: 10.3389/fmolb.2017.00092

[…] ver, the above models do not account for the heterogeneity of RNA conformations. Thus, in order to predict RNA structural changes, we need to sample RNA conformations using RNA folding models such as Vfold (Xu et al., ) and molecular dynamics (MD) simulations, and compute the ion-induced free energy changes for the different conformations. In what follows, we focus on the major conclusions and the […]

library_books

Nanopore electric snapshots of an RNA tertiary folding pathway

2017
Nat Commun
PMCID: 5684407
PMID: 29133841
DOI: 10.1038/s41467-017-01588-z

[…] A distinct feature of TS is the non-native tertiary interaction between stem Pʹ and the loop. The misfolded HP2 and TS structures are also supported by separate computational models. For example, the Vfold-based free energy analysis for the 2D structures and the SimRNA-based 3D structure analysis predicted TS and HP2 as misfolded suboptimal states of the sequence.Overall, the observations revealed […]

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

[…] interactions such as the kissing interaction of two hairpin loops. For example, most existing methods of RNA 3D structure prediction, such as fragment-assembling methods (FARNA/FARFAR (,), MC-Sym (), Vfold (), RNAComposer (), 3dRNA (), etc.), use local 3D templates to build the entire 3D structures. If the conformations of local 3D templates are inaccurate, the tertiary interactions, especially mu […]

library_books

Capturing RNA Folding Free Energy with Coarse Grained Molecular Dynamics Simulations

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

[…] s. Template based modeling uses predefined, small motifs to assemble RNA structures from their sequence. Template based 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 […]


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Vfold institution(s)
Department of Physics and Department of Biochemistry, University of Missouri, Columbia, MO, USA
Vfold funding source(s)
This research was supported by National Institutes of Health (NIH) grant GM063732 and National Science Foundation (NSF) grant MCB0920411.

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