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Protocols

FARNA specifications

Information


Unique identifier OMICS_16974
Name FARNA
Alternative name Function Annotation of human non-coding RNA transcripts
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Vladimir Bajic

Publication for Function Annotation of human non-coding RNA transcripts

FARNA citations

 (20)
library_books

LncRNA Structural Characteristics in Epigenetic Regulation

2017
Int J Mol Sci
PMCID: 5751261
PMID: 29292750
DOI: 10.3390/ijms18122659

[…] alignment []. Mainstream prediction software for the secondary structure prediction, include Pfold, RNAfold, RNAstructure, and more [,,,]. The toolkits for identifying the tertiary structure contain FaRNA, NAST, 3DRNA, and so forth [,,]. LncRNA structure prediction, with the development of RNA-sequence and high-throughput sequencing, comes into the era of structurome, and the efficiency and accur […]

library_books

Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide–nucleotide interactions from direct coupling analysis

2017
Nucleic Acids Res
PMCID: 5499770
PMID: 28482022
DOI: 10.1093/nar/gkx386

[…] anches and thus the tertiary interactions such as the kissing interaction of two hairpin loops. For example, most existing methods of RNA 3D structure prediction, such as fragment-assembling methods (FARNA/FARFAR (,), MC-Sym (), Vfold (), RNAComposer (), 3dRNA (), etc.), use local 3D templates to build the entire 3D structures. If the conformations of local 3D templates are inaccurate, the tertiar […]

library_books

Capturing RNA Folding Free Energy with Coarse Grained Molecular Dynamics Simulations

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

[…] deling 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 refinement available […]

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

[…] ternal loops and radii of gyration patterns, and are calculated based on known RNAs. This overall structure prediction combination has shown significant improvements over current approaches (NAST (), FARNA (,) and MC-Sym ()) for predicting 3D global helical arrangements in various RNAs computed as graphs (,). The final graph model was previously converted into an atomic model manually, but now thi […]

library_books

Structure Prediction of RNA Loops with a Probabilistic Approach

2016
PLoS Comput Biol
PMCID: 4975501
PMID: 27494763
DOI: 10.1371/journal.pcbi.1005032

[…] des a valuable alternative source of gaining structural information. Many programs have been developed to assist RNA 3D structure prediction, including YAMMP [], NAB [], ERNA-3D [], MANIP [], S2S [], FARNA [], MC-Fold/MC-Sym [], RNA2D3D [], iFoldRNA [, ], NAST [], Assemble [], HiRE-RNA [], FARFAR [], RNABuilder [], ModeRNA [], OxRNA [], 3dRNA [], a coarse-grained model that includes salt effect [] […]

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

[…] y using a generic library for single-stranded, protein-bound ssRNA trinucleotides that occur in nature. However, to the best of our knowledge, no such library exists. The RNA fragment library used by FARNA for de novo prediction of RNA was built “from a single crystal structure containing just over 2,700 ribonucleotides from the large ribosomal subunit from Haloarcula marismortui [1FFK]” [], which […]

Citations

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FARNA institution(s)
King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
FARNA funding source(s)
This work was supported by King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) [URF/1/1976-04]; KAUST base research funds.

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