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Protocols

RAGTOP specifications

Information


Unique identifier OMICS_23615
Name RAGTOP
Alternative name RNA-As-Graph-TOPologies
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Tamar Schlick

Publications for RNA-As-Graph-TOPologies

RAGTOP citations

 (4)
library_books

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

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

[…] s capabilities relies on its sampling scheme, which allows displacements of large RNA domains, motions that cannot be efficiently sampled under atomistic approaches. At a similar level of resolution, RAGTOP builds 3D graphs from a given secondary structure. Junctions between helices are predicted first, and a subsequent simulated annealing optimizes the structure subjected to knowledge-based poten […]

call_split

Computational Methods for Modeling Aptamers and Designing Riboswitches

2017
Int J Mol Sci
PMCID: 5713409
PMID: 29149090
DOI: 10.3390/ijms18112442
call_split See protocol

[…] um double glycine riboswitch as an example, the Rosetta 3D modeling can give a similar prediction as RMdetect and JAR3D [,,,].Also, starting from 2D structures, a hierarchical computational approach (RAGTOP) was modified to predict 10 representative riboswitch aptamers with diverse structural features [], by combining the coarse-grained graph sampling approach []. Through integration of computatio […]

library_books

Capturing RNA Folding Free Energy with Coarse Grained Molecular Dynamics Simulations

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

[…] In graph theory techniques, RNA is depicted topologically to build RNA structures; this improves sampling and even allows for creation of novel RNA motifs. Graph theory techniques are utilized by RAG/RAGTOP and others. In physics based methods, the RNA is built from sequence into a 3D structure, and these 3D RNA structures are sampled using Monte Carlo or Molecular Dynamics (MD) protocols. Due to […]

call_split

Using sequence signatures and kink turn motifs in knowledge based statistical potentials for RNA structure prediction

2017
Nucleic Acids Res
PMCID: 5435971
PMID: 28158755
DOI: 10.1093/nar/gkx045
call_split See protocol

[…] Here we describe: (i) annotation of the k-turn motifs by DSSR for a priori potential calculations, (ii) resulting potentials for k-turn and other remaining internal loops and (iii) RAGTOP protocol with annotation of the k-turn motifs by conserved sequence and secondary structure analysis of internal loops. […]

Citations

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RAGTOP institution(s)
Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
RAGTOP funding source(s)
Supported by the National Institutes of Health (GM100469, GM081410).

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