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Protocols

RNA FRABASE specifications

Information


Unique identifier OMICS_04456
Name RNA FRABASE
Restrictions to use None
Database management system PostgreSQL
Community driven No
Data access Browse
User data submission Not allowed
Version 2.0
Maintained Yes

Maintainer


  • person_outline Marta Szachniuk

Publications for RNA FRABASE

RNA FRABASE citations

 (6)
library_books

Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools

2018
Front Genet
PMCID: 5780412
PMID: 29403526
DOI: 10.3389/fgene.2017.00231

[…] a to strengthen the 3D predictions. The secondary structure is divided into fragments containing overlapping canonical base pairs to build the model. The fragments are related to 3D elements found in RNA FRABASE database (Popenda et al., , ), which is a dictionary containing RNA 3D structure elements derived from structures deposited in the RCSB PDB. RNAComposer automatically assembles the 3D elem […]

library_books

Selection and targeting of EpCAM protein by ssDNA aptamer

2017
PLoS One
PMCID: 5731996
PMID: 29245156
DOI: 10.1371/journal.pone.0189558

[…] ://rnacomposer.ibch.poznan.pl/Home) for entirely automated prediction of the aptamer 3-D structures. RNA Composer server performs according to the principle of translation machine and executes on the RNA FRABASE database. RNA FRABASE is a search engine associated with database of RNA 3-D structures, which depends as an input on secondary structure in the dot-bracket notation (Vienna format). Secon […]

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

[…] ded into stems, loops, and single strands in the program. 3D structure elements corresponding to these fragmentations are searched within the structure elements dictionary, which is tailored from the RNA FRABASE database and consists of a 3D structural element with good structural properties []. After the searching process, the 3D elements whose heavy-atom root mean square deviation (RMSD) is lowe […]

library_books

The Combination of Computational and Biosensing Technologies for Selecting Aptamer against Prostate Specific Antigen

2017
Biomed Res Int
PMCID: 5387809
PMID: 28459059
DOI: 10.1155/2017/5041683

[…] DNA aptamers. The method used by the RNAComposer web server is based on the machine translation principle and needs the information of secondary structure provided by RNAfold, and it operates on the RNA FRABASE database. After getting the RNA model generated by the RNAComposer web server, we used Accelrys Discovery Studio (DS) 4.1 to edit the pyrimidine bases in the structure file to make uracil […]

call_split

New in silico approach to assessing RNA secondary structures with non canonical base pairs

2015
BMC Bioinformatics
PMCID: 4557229
PMID: 26329823
DOI: 10.1186/s12859-015-0718-6
call_split See protocol

[…] ndary structure. For the purpose of our research we have selected RNAComposer [] — a web server tool for fast, fully automated, high-throughput modeling of large RNA 3D structures. It operates on the RNA FRABASE database [], acting as a dictionary that relates the RNA secondary and tertiary structure elements. The output RNA model is composed by assembling the 3D fragments, which carry the knowled […]

library_books

Sequence–structure relationships in RNA loops: establishing the basis for loop homology modeling

2009
Nucleic Acids Res
PMCID: 2817452
PMID: 19923230
DOI: 10.1093/nar/gkp1010

[…] mples of current RNA 3D structural motif databases that can form a possible foundation for such a knowledge base are the Structural Classification of RNA database (), the RNAjunction database (), the RNA FRABASE () and the DARTS database (). Second, the sequence–structure relationships have to be explored. Up to what degree of sequence divergence can RNA loops be expected to assume a similar struc […]

Citations

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RNA FRABASE institution(s)
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Poznan, Poland; Poznan Supercomputing and Networking Centre, Poznan, Poland; Automated Scheduling, Optimisation and Planning Group, School of Computer Science, University of Nottingham, Nottingham, UK
RNA FRABASE funding source(s)
Supported by Polish Ministry of Science and Higher Education [PBZ-MniSW-07/1/ 2007/01, NN 519314635], and the Erasmus fellowships to at the University of Nottingham.

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