Abstract
The relaxation matrix for a macromolecule is a 2D array holding the set of auto and cross relaxation rates. This is used in the numerical simulation of NOEs for given candidate structures. Structure refinement routines that compare experimental and simulated NOEs require many recalculations of the matrix and algorithm efficiency should be an important consideration. Three algorithms are described and their relative efficiencies compared by computing relaxation matrices for model macromolecules. An interaction distance cutoff of 8 Angstroms greatly reduces the calculation time for large systems and introduces only a small truncation error. Further performance improvements, at the same level of accuracy, were obtained by using a 3D array/linked list data structure to avoid calculating the full set of N(N — 1)/2 distances.
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© 1991 Springer Science+Business Media New York
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Forster, M.J. (1991). Fast Calculation of the Relaxation Matrix. In: Hoch, J.C., Poulsen, F.M., Redfield, C. (eds) Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy. NATO ASI Series, vol 225. Springer, Boston, MA. https://doi.org/10.1007/978-1-4757-9794-7_30
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DOI: https://doi.org/10.1007/978-1-4757-9794-7_30
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4757-9796-1
Online ISBN: 978-1-4757-9794-7
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