Efficient Calculation of Molecular Configurational Entropies Using an Information Theoretic Approximation
Author(s)King, Bracken Matheny; Silver, Nathaniel W.; Tidor, Bruce
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Accurate computation of free energy changes upon molecular binding remains a challenging problem, and changes in configurational entropy are especially difficult due to the potentially large numbers of local minima, anharmonicity, and high-order coupling among degrees of freedom. Here we propose a new method to compute molecular entropies based on the maximum information spanning tree (MIST) approximation that we have previously developed. Estimates of high-order couplings using only low-order terms provide excellent convergence properties, and the theory is also guaranteed to bound the entropy. The theory is presented together with applications to the calculation of the entropies of a variety of small molecules and the binding entropy change for a series of HIV protease inhibitors. The MIST framework developed here is demonstrated to compare favorably with results computed using the related mutual information expansion (MIE) approach, and an analysis of similarities between the methods is presented.
DepartmentMassachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory; Massachusetts Institute of Technology. Department of Biological Engineering; Massachusetts Institute of Technology. Department of Chemistry; Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
The Journal of Physical Chemistry B
American Chemical Society (ACS)
King, Bracken M., Nathaniel W. Silver, and Bruce Tidor. “Efficient Calculation of Molecular Configurational Entropies Using an Information Theoretic Approximation.” The Journal of Physical Chemistry B 116, no. 9 (March 8, 2012): 2891–2904.
Author's final manuscript