RNA-MoIP statistics

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Protocols

RNA-MoIP specifications

Information


Unique identifier OMICS_18500
Name RNA-MoIP
Alternative name RNA Motifs over Integer Programming
Interface Web user interface
Restrictions to use None
Input data An RNA sequence or a set of RNA sequences.
Input format FASTA
Output data An image of the corrected secondary structure and location of inserted motifs are generated.
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Jerome Waldispuhl

Publication for RNA Motifs over Integer Programming

RNA-MoIP citations

 (6)
library_books

Capturing RNA Folding Free Energy with Coarse Grained Molecular Dynamics Simulations

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

[…] late 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 refinem […]

call_split

Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment Based Approach

2016
PLoS Comput Biol
PMCID: 4729675
PMID: 26815409
DOI: 10.1371/journal.pcbi.1004697
call_split See protocol

[…] taining just over 2,700 ribonucleotides from the large ribosomal subunit from Haloarcula marismortui [1FFK]” [], which is mainly double-stranded. The libraries used by MC-Fold/MC-Sym [] ModeRNA [] or RNA-MoIP [] represent only fragments that are partially or fully double-stranded fragments (“Nucleotide Cyclic Motifs”) [] or internal loops (which limit the backbone conformations sampling by a loop […]

library_books

RNA 3D Modules in Genome Wide Predictions of RNA 2D Structure

2015
PLoS One
PMCID: 4624896
PMID: 26509713
DOI: 10.1371/journal.pone.0139900

[…] ly time-consuming and limited to small molecules. Laing and Schlick reviewed these where they explore new ideas towards 3D structure prediction []. Reinharz et al. [] developed an automated pipeline, RNA-MoIP, for combining 2D and 3D information to refine tertiary predictions. In a first step, they use a classical secondary structure predictor to get a set of sub-optimal structures. In a second st […]

call_split

Modeling the Structure of RNA Molecules with Small Angle X Ray Scattering Data

2013
PLoS One
PMCID: 3817170
PMID: 24223750
DOI: 10.1371/journal.pone.0078007
call_split See protocol

[…] quence and secondary structure. Of these, MC-SYM uses least-squares minimization of cyclic motif networks, ASSEMBLE allows for hand-picking of the most appropriate motifs using human knowledge, and RNA-MoIP uses an integer programming framework in order to scale to larger RNA molecules.There have also been several attempts to develop conventional sequential fragment assembly, which works by cop […]

library_books

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments

2013
Nucleic Acids Res
PMCID: 3905863
PMID: 24005040
DOI: 10.1093/nar/gkt795

[…] putationally less costly secondary structure prediction. For example, () enhances the 3D structure prediction of large RNAs by inserting 3D modules into the secondary structure. Their program, called RNA-MoIP, uses an integer programming framework to remove canonical base pairs from secondary structures to make room for 3D modules (e.g. k-way junctions), which serve as a template for creating a 3D […]

call_split

Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure

2012
Bioinformatics
PMCID: 3371858
PMID: 22689763
DOI: 10.1093/bioinformatics/bts226
call_split See protocol

[…] t ω be a RNA sequence. First, we use a classical secondary structure predictor (e.g. RNAsubopt) to generate a list of sub-optimal secondary structures. Second, for each structure from the list we use RNA-MoIP to insert RNA 3D motifs in the structure using the sequence information provided by ω. RNA-MoIP works in two steps: Given a database of sequences of RNA 3D motifs (cf. ), the preprocessing st […]

Citations

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RNA-MoIP institution(s)
School of Computer Science, McGill University, Montreal, QC, Canada; Department of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Institute for Research in Immunology and Cancer and Department of Computer Science and Operations Research, Université de Montreal, Montreal, QC, Canada
RNA-MoIP funding source(s)
Supported by Natural Sciences and Engineering Research Council of Canada (NSERC) [RGPIN 2015-03786 & RGPAS 477873- 15]; Canadian Institutes of Health Research (CHIR) [CIHR BOP-149429]; Genome Canada [B/CB 2015]; Natural Sciences and Engineering Research Council of Canada USRA and Fonds de recherche du Quebec, Nature et technologies BRPC fellowships; Azrieli and Fonds de recherche du Quebec Nature et technologies postdoctoral fellowships; Canadian Institutes of Health Research (CIHR) [MT-14604]; National Institutes of Health (NIH) [R01GM088813]; and Natural Sciences and Engineering Research Council of Canada (NSERC) [170165-01].

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