QCRNA 1.0: A database of quantum calculations for RNA catalysis

Journal of Molecular Graphics and Modelling vol. 25  p. 423-433  DOI: 10.1016/j.jmgm.2006.02.011
PMID/PMCID: 16580853 Published: 2006-10-01 

Timothy J. Giese [ ] , Brent A. Gregersen, Yun Liu, Kwangho Nam, Evelyn Mayaan, Adam Moser, Kevin Range, Olalla Nieto-Faza, Carlos Silva-Lopez, Angel Rodriguez de Lera, Gijs Schaftenaar, Xabier Lopez, Tai-Sung Lee [ ] , George Karypis, Darrin M. York [ ]

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This work outlines a new on-line database of quantum calculations for RNA catalysis (QCRNA) available via the worldwide web at http://theory.rutgers.edu/QCRNA/. The database contains high-level density functional calculations for a large range of molecules, complexes and chemical mechanisms important to phosphoryl transfer reactions and RNA catalysis. Calculations are performed using a strict, consistent protocol such that a wealth of cross-comparisons can be made to elucidate meaningful trends in biological phosphate reactivity. Currently, around 2000 molecules have been collected in varying charge states in the gas phase and in solution. Solvation was treated with both the PCM and COSMO continuum solvation models. The data can be used to study important trends in reactivity of biological phosphates, or used as benchmark data for the design of new semiempirical quantum models for hybrid quantum mechanical/molecular mechanical simulations.