RNABP COGEST: a resource for investigating functional RNAs

Database : the Journal of Biological Databases and Curation
Sohini BhattacharyaAbhijit Mitra

Abstract

Structural bioinformatics of RNA has evolved mainly in response to the rapidly accumulating evidence that non-(protein)-coding RNAs (ncRNAs) play critical roles in gene regulation and development. The structures and functions of most ncRNAs are however still unknown. Most of the available RNA structural databases rely heavily on known 3D structures, and contextually correlate base pairing geometry with actual 3D RNA structures. None of the databases provide any direct information about stabilization energies. However, the intrinsic interaction energies of constituent base pairs can provide significant insights into their roles in the overall dynamics of RNA motifs and structures. Quantum mechanical (QM) computations provide the only approach toward their accurate quantification and characterization. 'RNA Base Pair Count, Geometry and Stability' (http://bioinf.iiit.ac.in/RNABPCOGEST) brings together information, extracted from literature data, regarding occurrence frequency, experimental and quantum chemically optimized geometries, and computed interaction energies, for non-canonical base pairs observed in a non-redundant dataset of functional RNA structures. The database is designed to enable the QM community, on the one hand, ...Continue Reading

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Citations

Jan 20, 2017·Journal of Computer-aided Molecular Design·Dhananjay BhattacharyyaManju Bansal
Sep 19, 2015·Physical Chemistry Chemical Physics : PCCP·Antarip HalderAbhijit Mitra
Aug 9, 2018·Physical Chemistry Chemical Physics : PCCP·Antarip HalderAbhijit Mitra
Oct 19, 2017·Physical Chemistry Chemical Physics : PCCP·Satyabrata Maiti, Dhananjay Bhattacharyya
Sep 20, 2019·Physical Chemistry Chemical Physics : PCCP·Manas MondalYi Qin Gao

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Methods Mentioned

BETA
X-ray

Software Mentioned

RNAS
RNA Base Pair Count , Geometry and Stability ( RNABP COGEST )
NUPARM
RNABPCOGEST
BPFIND
MySQL
RNABP COGEST
HD
JQuery
webFR3D

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