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RAG specifications

Information


Unique identifier OMICS_28145
Name RAG
Alternative name Rna-As-Graphs
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Tamar Schlick

Additional information


http://www.biomath.nyu.edu/RAG3D/help

Publications for Rna-As-Graphs

RAG citations

 (5)
library_books

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

[…] NAs (), and assembling RNAs from fragments (). Here, we focus on our recent application of predicting tertiary topologies of RNAs from given or predicted secondary structures using RAGTOP.The RAGTOP (RNA-As-Graphs-Topologies) hierarchical graph sampling approach has shown promise for characterizing 3D helical arrangements in RNAs and predicting riboswitch 3D structures from a given 2D structure re […]

library_books

Accurate Classification of RNA Structures Using Topological Fingerprints

2016
PLoS One
PMCID: 5068708
PMID: 27755571
DOI: 10.1371/journal.pone.0164726

[…] es, containing pseudoknots, and with little sequence similarity. Topological methods have the dual advantage of easily representing pseudoknots and not requiring an insertion/deletion penalty. In the RNA-As-Graphs procedure [, , , ], RNA topologies are represented either as “tree graphs” (without pseudoknots) or “dual graphs” (with pseudoknots), and the topological properties of an RNA graph are s […]

library_books

Viral RNAs Are Unusually Compact

2014
PLoS One
PMCID: 4154850
PMID: 25188030
DOI: 10.1371/journal.pone.0105875

[…] embles with 1000 configurations of each RNA were calculated using the RNAsubopt program in Vienna as described in earlier work . Each secondary structure in the ensemble was then converted using the RNA-As-Graphs program , into the Laplacian matrix representing the corresponding tree graph. Adjacency and degree matrices were deduced from the Laplacian for further analyses. Degree matrices were u […]

library_books

Classifying Multigraph Models of Secondary RNA Structure Using Graph Theoretic Descriptors

2012
ISRN Bioinform
PMCID: 4393061
PMID: 25969746
DOI: 10.5402/2012/157135

[…] cal ones []. Other means of characterizing the topology of secondary RNA structures are still an active avenue of pursuit.The graph representations used in this work can be found in the database RAG: RNA-As-Graphs []. Secondary RNA structure is modeled by two graph-theoretic representations in the database resource RAG (see [] for additional details on the differences between the two). In one of t […]

library_books

A predictive model for secondary RNA structure using graph theory and a neural network

2010
BMC Bioinformatics
PMCID: 3026369
PMID: 20946605
DOI: 10.1186/1471-2105-11-S6-S21

[…] egrates thermodynamic and phylogenetic information in a modified energetic model. There is general agreement that there is still room for improvement in each of these approaches []. The database RAG: RNA-As-Graphs represents secondary RNA using graph theory []. The details of the graph-theoretic representation are provided in the following section. We utilize the information in the RAG database to […]

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RAG institution(s)
Department of Chemistry, New York University, New York, NY, USA; Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
RAG funding source(s)
Supported by the National Science Foundation (DMS-0201160, CCF-0727001) and the National Institute of Health (GM081410).

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