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Empirical energy functions for energy minimization and dynamics of nucleic acids
Author(s) -
Nilsson Lennart,
Karplus Martin
Publication year - 1986
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540070502
Subject(s) - random hexamer , nucleic acid , sublimation (psychology) , chemistry , molecular dynamics , energy minimization , potential energy , sugar phosphates , chemical physics , computational chemistry , crystallography , atomic physics , phosphate , physics , organic chemistry , biochemistry , psychology , psychotherapist
An improved empirical energy function for energy minimization and dynamics calculations of nucleic acids is developed and evaluated by an examination of its representation of both static and dynamic properties of model systems. Among the properties studied and used for parameter optimization are base pairing interactions, sugar and phosphate energy surfaces, small crystal heats of sublimation, base, phosphate and sugar analogue vibration spectra, and the overall behavior of a DNA hexamer duplex in vacuum molecular dynamics simulations. The results obtained are compared with those from two other energy functions that have been used recently for nucleic acids. Parameters for two energy functions are given; one includes heavy atoms and only polar hydrogens and the other includes all atoms.