Kernel energy method: application to DNA.

Lulu Huang; Lou Massa; Jerome Karle

doi:10.1021/bi051655l

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Kernel energy method: application to DNA.

Lulu Huang·Lou Massa·Jerome Karle

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Abstract

The kernel energy method (KEM) has been used in three recent papers (1-3) to calculate the quantum mechanical ab inito molecular energy of peptides and the protein insulin. It was found to have good accuracy. The computational difficulty of representing a molecule increases only modestly with the number of atoms. The calculations are simplified by adopting the approximation that a full biological molecule can be represented by smaller "kernels" of atoms. In this paper, the accuracy of the KEM is tested in the application to DNA, whose basic kernels, chemical bonding, and overall molecular structure are quite different from peptides and proteins. The basic kernel in the case of peptides and proteins is an amino acid. The basic kernel in the case of DNA is a nucleotide consisting of a phosphate-sugar-base. The molecular energy is calculated for all three basic types of DNA, i.e., B, A, and Z configurations of DNA. The results give an accuracy that is comparable to that achieved with peptides and proteins. Thus, the KEM is found to be applicable to major types of biological molecules.

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Base Sequence DNA Insulin Nucleic Acid Conformation Peptides Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

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Lulu Huang, Lou Massa, Jerome Karle. 2005-12-20. Kernel energy method: application to DNA.. https://doi.org/10.1021/bi051655l

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