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RNA Base Pair Count Geometry and Stability (RNABP COGEST) : a database of QM analysis data of RNA base pairsAuthors: Sohini Bhattacharya, Shriyaa Mittal, Swati Panigrahi,Abhijit Mitra, Dhananjay Bhattacharyya Conference: 7th. RNA Group Meeting Location Indian Institute of Chemical Biology, Kolkata Date: 2014-03-06 Report no: IIIT/TR/2014/43 AbstractHydrogen bonded non-canonical base pairs have been identified as the key player behind the
structural complexity and functional diversity of the RNA molecule. Enormous research have been
performed to understand the correlation between different base pairing geometries and their
contributions in the overall structural stabilities and functionalities. Towards this goal, calculation of
intrinsic interaction energy of different base pairing geometries using ab-initio and DFT based
Quantum Mechanical methods provide a significant insight in the context of RNA. Analysis of
deviation in geometry and intrinsic interaction energy between the crystal and ground state optimized
structures reveal the chemical behaviours of a particular base pair and the contextual effects on its
stability. Fueled by the advancement of post Hartree-Fock QM theories and more accurate basis sets,
the present knowledge base is flooded with a large amount of QM analysis data which lacks the
systematic organization and hence fails to serve the scientific community in the best possible way. We,
therefore, have attempted to build a relational database, “RNA Base Pair Count Geometry and Stability
(RNABP COGEST)”, which relates the occurrence frequencies of different base pairs in RNA with
their crystal and ground state optimized geometries (calculated at different levels of QM theory) and
corresponding intrinsic interaction energies. To the best of our knowledge, this is the first attempt to
organize energetics information for different RNA base pairs along with their occurrences and
geometries. Our database provides an interactive interface which enables the user to extract data by
constructing diverse geometry, frequency and energy based search queries for the purpose of better
understanding of the complex relation between the geometry and stability of RNA base pairs. Full paper: pdf Centre for Computational Natural Sciences and Bioinformatics |
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