Jerome Karle (2006) - Kernel Energy Method Illustrated with Peptides

Jerome Karle (2006)

Kernel Energy Method Illustrated with Peptides

Jerome Karle (2006)

Kernel Energy Method Illustrated with Peptides

Abstract

A Kernel Energy Method (KEM), for applying quantum crystallography to large molecules is described. Application has usually concerned the calculation of the molecular energy of peptides, is described. The computational difficulty of representing the system increases only modestly with the number of atoms. The calculations are carried out on modern parallel supercomputers. By adopting the approximation that a full biological molecule can be represented by smaller "kernels" of atoms, the calculations are greatly simplified.

Collections of kernels are, from a computational point of view, well suited for parallel computation. The result is a modest increase in computational time as the number of atoms increases, while retaining the ab-initio character of the calculations. A test of the method and its accuracy is illustrated with the use of 15 different peptides of biological interest.

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