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Assessing the performance of computational methods for the prediction of the ground state structure of a cyclic decapeptide

Publication Type : Journal Article

Publisher : International Journal of Quantum Chemistry

Source : International Journal of Quantum Chemistry, John Wiley & Sons Inc., Volume 113, Number 6, p.808–814 (2012)

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Keywords : cold ion spectroscopy, Density functional theory, density functional tight-binding, force field, Peptides

Campus : Amritapuri, Bengaluru

School : School of Biotechnology, School of Engineering

Department : Computer Science

Year : 2012

Abstract : We benchmark the performance of various computational approaches, ranging from the classical nonpolarizable force fields AMBER FF96 and FF99SB, the polarizable force fields AMBER FF02polEP and AMOEBAbio09 to the semiempirical DFT method SCC-DFTB. The test set consists of nine conformations of gas-phase protonated gramicidin S, a cyclic decapeptide. We discuss their structural features in relation to the intrinsic lowest energy structure, which has been solved recently by a combination of cold ion spectroscopy and high level theoretical methods (Nagornova et al., Angew Chem Int Ed 2011, 50, 5383). As a reference, we use the energetics at the M05-2X level of theory. The latter has been validated as a suitable reference method in predicting the correct ground state structure of gas-phase protonated bare and microsolvated tryptophan as well as gas-phase protonated gramicidin S by comparison to experiment. We discuss the performance of the different more approximate methods in relation to their potential use as efficient and reliable tools to explore conformational space for the generation of candidate structures before refinement at the DFT level.

Cite this Research Publication : M. Doemer, Guglielmi, M., Dr. Prashanth Athri, Nagornova, N. S., Rizzo, T. R., Boyarkin, O. V., Tavernelli, I., and Rothlisberger, U., “Assessing the performance of computational methods for the prediction of the ground state structure of a cyclic decapeptide”, International Journal of Quantum Chemistry, vol. 113, pp. 808–814, 2012.

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