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Protocols

RNA Bricks specifications

Information


Unique identifier OMICS_06131
Name RNA Bricks
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Grzegorz Chojnowski

Publication for RNA Bricks

RNA Bricks citations

 (3)
call_split

Impact of the structural integrity of the three way junction of adenovirus VAI RNA on PKR inhibition

2017
PLoS One
PMCID: 5650172
PMID: 29053745
DOI: 10.1371/journal.pone.0186849
call_split See protocol

[…] re predicted using RNA Masonry, a new method based on software developed in the Bujnicki laboratory, including the SimRNA method for RNA folding [] and the library of recurrent 3D motifs available in RNA Bricks database []. Briefly, RNA Masonry uses the energy function established for the SimRNA method [], and composes atomistic models by assembling existing fragments using a replica exchange Mont […]

library_books

CompAnnotate: a comparative approach to annotate base pairing interactions in RNA 3D structures

2017
Nucleic Acids Res
PMCID: 5737500
PMID: 28641399
DOI: 10.1093/nar/gkx538

[…] ervations for RNA depend on the different characteristics of these interactions (–). Finding and categorizing RNA structural motifs is one significant example of such research. Tools such as FR3D (), RNA Bricks (), RNAMotifScan (), RNAMotifScanX () deal with this issue and are largely built upon base-pairing annotation. Another relevant research is aligning RNA structures. Base-pairing annotation […]

library_books

The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection

2013
Nucleic Acids Res
PMCID: 3965027
PMID: 24316579
DOI: 10.1093/nar/gkt1282

[…] revious years, this Database Issue features an impressive selection of structural databases. Two of them deal with nucleic acid structure: an update on the well-known Nucleic Acids Database (NDB) and RNA Bricks, a new database of RNA 3D motifs and their contacts (,). The block of protein structure databases includes, among others, updates on Protein Data Bank in Europe (PDBe), PDBsum, ArchDB, Gene […]

Citations

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RNA Bricks institution(s)
International Institute of Molecular and Cell Biology, Warsaw, Poland; Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw, Poland; Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland

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