MC-Sym statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

MC-Sym specifications

Information


Unique identifier OMICS_22762
Name MC-Sym
Alternative name Macromolecular Conformations by SYMbolic programming
Software type Application/Script
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Francois Major

Additional information


http://www.major.iric.ca/wiki/index.php/MC-Sym http://www.major.iric.ca/MC-Sym/faq.html

Publication for Macromolecular Conformations by SYMbolic programming

MC-Sym citations

 (60)
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 nucleo […]

library_books

Combined roles of ATP and small hairpin RNA in the activation of RIG I revealed by solution based analysis

2018
Nucleic Acids Res
PMCID: 5887321
PMID: 29346611
DOI: 10.1093/nar/gkx1307

[…] ly determined structure of DC-RIG-I/8 bp complex (PDB ID: 4AY2) was used as a starting point, however, the 8-base pair dsRNA in the crystal structure was replaced by a 10-base pair dsRNA generated by MC-Sym pipeline (). In the case of DC-RIG-I/10 bp/ADP-AlFx, a best fitting model was generated when all domains were kept rigid against the SAXS data, but for DC-RIG-I/10 bp or DC-RIG-I/10 bp/AMP-PNP […]

library_books

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs

2018
Front Microbiol
PMCID: 5758548
PMID: 29354101
DOI: 10.3389/fmicb.2017.02582

[…] as done for Zika virus, or combination of prediction programs as was used to predict a functional pseudoknot in West Nile virus (Moomau et al., ). Models in 3D can be built of pseudoknots e.g., using MC-Sym as was recently done for Venezuelan equine encephalitis virus (Kendra et al., ). […]

library_books

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

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

[…] 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 among othe […]

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

[…] 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 that it s […]

library_books

A non canonical site reveals the cooperative mechanisms of microRNA mediated silencing

2017
Nucleic Acids Res
PMCID: 5499589
PMID: 28482037
DOI: 10.1093/nar/gkx340

[…] ALG-1 overall and 94% identity within the MID/PIWI domains (). We then modeled the RNA duplex structures of miR-80 (a Bantam family miRNA) and miR-35 with their cognate toh-1 binding sites using the MC-Sym algorithm (). Each duplex was docked in ALG-2 in an ‘open’ conformation obtained through an elastic network model that simulates relative motions of the lobes in the protein structure that have […]

Citations

Looking to check out a full list of citations?

MC-Sym institution(s)
Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, QC, Canada
MC-Sym funding source(s)
Supported by grants from Canadian Institutes of Health Research (CIHR) and from the Natural Sciences and Engineering Research Council (NSERC) of Canada.

MC-Sym reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review MC-Sym