"Mining Minima": Direct Computation of Conformational Free Energy

by: MS Head, JA Given, MK Gilson

J. Phys. Chem. A, Vol. 101, No. 8. (20 February 1997), pp. 1609-1618.

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DOI, American Chem. Soc. Publications

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Abstract

Abstract: We describe a novel, two-step method for directly computing the conformational free energy of a molecule. In the first step, a finite set of low-energy conformations is identified, and its contribution to the configuration integral is evaluated by a straightforward Monte Carlo technique. The method of finding energy minima incorporates certain features of the global-underestimator method and of a genetic algorithm. In the second step, the contribution to the configuration integral due to conformations not included in the initial integration is determined by Metropolis Monte Carlo sampling. Applications to alanine oligopeptides and to three cyclic urea inhibitors of HIV protease are presented.

@article{citeulike:2627780, abstract = {Abstract: We describe a novel, two-step method for directly computing the conformational free energy of a molecule. In the first step, a finite set of low-energy conformations is identified, and its contribution to the configuration integral is evaluated by a straightforward Monte Carlo technique. The method of finding energy minima incorporates certain features of the global-underestimator method and of a genetic algorithm. In the second step, the contribution to the configuration integral due to conformations not included in the initial integration is determined by Metropolis Monte Carlo sampling. Applications to alanine oligopeptides and to three cyclic urea inhibitors of HIV protease are presented.}, address = {Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850}, author = {Head, M. S. and Given, J. A. and Gilson, M. K. }, citeulike-article-id = {2627780}, doi = {10.1021/jp963817g}, journal = {J. Phys. Chem. A}, keywords = {free\_energy}, month = {February}, number = {8}, pages = {1609--1618}, posted-at = {2008-04-03 20:52:59}, priority = {2}, title = {"Mining Minima": Direct Computation of Conformational Free Energy}, url = {http://dx.doi.org/10.1021/jp963817g}, volume = {101}, year = {1997} }

RIS record

TY - JOUR ID - citeulike:2627780 L3 - citeulike-article-id:2627780 TI - "Mining Minima": Direct Computation of Conformational Free Energy JF - J. Phys. Chem. A VL - 101 IS - 8 SP - 1609 EP - 1618 AD - Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850 N2 - Abstract: We describe a novel, two-step method for directly computing the conformational free energy of a molecule. In the first step, a finite set of low-energy conformations is identified, and its contribution to the configuration integral is evaluated by a straightforward Monte Carlo technique. The method of finding energy minima incorporates certain features of the global-underestimator method and of a genetic algorithm. In the second step, the contribution to the configuration integral due to conformations not included in the initial integration is determined by Metropolis Monte Carlo sampling. Applications to alanine oligopeptides and to three cyclic urea inhibitors of HIV protease are presented. KW - free_energy AU - Head, MS AU - Given, JA AU - Gilson, MK PY - 1997/02/20/ UR - http://dx.doi.org/10.1021/jp963817g ER -

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