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Protocols

MC-Fold specifications

Information


Unique identifier OMICS_04467
Name MC-Fold
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Input data An RNA sequence.
Output data A list of tuples of sequences and one of their associated secondary structures.
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Publication for MC-Fold

MC-Fold citations

 (57)
call_split

Translation initiation of alphavirus mRNA reveals new insights into the topology of the 48S initiation complex

2018
Nucleic Acids Res
PMCID: 5934618
PMID: 29415133
DOI: 10.1093/nar/gky071
call_split See protocol

[…] or sequencing. Fragments were analyzed in 10% acrylamide-urea gels and bands were quantified by densitometry and normalized. SHAPE data were used as constraints to generate 2D and 3D models using the MC-fold and RNAComposer pipelines (). RNAfold (Vienna RNA Web Services) was routinely used to calculate the minimal folding energy of centroid RNA structures and base pair probabilities. […]

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

[…] MC-Sym provides tertiary structures using the MC-Fold's secondary structures (Parisien and Major, ). The RNA-structure-prediction method is based on Nucleotide Cyclic Motifs (NCM), in which all nucleotides in fragments are circularly connected by […]

library_books

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

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

[…] ructures of given sequences. Authors of the Vfold, SimRNA, and DMD models have participated very actively in this challenge, as have the creators of other all-atom methods such as FARFAR, RNABuilder, MC-Fold/MC-Sym pipeline, and RNA123. Although most of the predictions are performed using hybrid approaches that involve experimental inputs, constraints for 2D structures, and all-atom refinements am […]

library_books

Selection and targeting of EpCAM protein by ssDNA aptamer

2017
PLoS One
PMCID: 5731996
PMID: 29245156
DOI: 10.1371/journal.pone.0189558

[…] MC-fold web server, (http://www.major.iric.ca/MC-Fold/) was used for prediction of Ep1 aptamer secondary folding structure and hybridization. Aptamer structure with the minimum energy (the lowest ΔG v […]

call_split

A to I editing in human miRNAs is enriched in seed sequence, influenced by sequence contexts and significantly hypoedited in glioblastoma multiforme

2017
Sci Rep
PMCID: 5446428
PMID: 28550310
DOI: 10.1038/s41598-017-02397-6
call_split See protocol

[…] tructural analysis, 18 candidate miRNAs were chosen (Supplemental Table ) and the optimal secondary structure in dot-bracket notation (from RNAfold WebServer) was used as structural constrains in the MC-Fold | MC-Sym pipeline. Structural constrains forces certain nucleotides to be either paired or unpaired and will restrict the conformational search space. The advantage of using a dual approach is […]

library_books

Capturing RNA Folding Free Energy with Coarse Grained Molecular Dynamics Simulations

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

[…] sed modeling to sample and predict relevant 3-D RNA structures. 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 […]

Citations

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MC-Fold institution(s)
Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, QC, Canada
MC-Fold funding source(s)
Supported by the Canadian Institutes of Health Research (CIHR), the Natural Sciences and Engineering Research Council (NSERC) of Canada and the NSERC and the Fonds Quebecois de la Recherche sur la Nature et les Technologies.

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