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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

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Maintainer


  • person_outline Shi-Jie Chen <>

Publication for Vfold

Vfold in publications

 (11)
PMCID: 5684407
PMID: 29133841
DOI: 10.1038/s41467-017-01588-z

[…] 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 […]

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

[…] 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 […]

PMCID: 5385882
PMID: 28393861
DOI: 10.1038/srep45812

[…] 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 […]

PMCID: 5389472
PMID: 28082395
DOI: 10.1093/nar/gkw1351

[…] rapidly appeared to be a singularity of the crystal structure. during the molecular replacement process, many models were built with available web facilities, such as assemble (), rnacomposer (), vfold-3d () and mc-fold (). all those models were more bent than the observed structure in the present crystals, some of them as much as an ‘l’. this is also the case of a solution structure obtained […]

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

[…] flaws in the energy function for a testing set of 15 rna loops []. liu and chen designed a set of dinucleotide-based statistical potentials for rna loops and junctions and combined them with their vfold model, then they made predictions for the coarse-grained (cg) 3d structures of both rna loops and junctions []. one unique advantage of their approach is its ability to go beyond the native […]


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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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