''Mining minima'': Direct computation of conformational free energy

被引：120

作者：

Head, MS ^{[1
]}

Given, JA ^{[1
]}

Gilson, MK ^{[1
]}

机构：

[1] NIST,CTR ADV RES BIOTECHNOL,ROCKVILLE,MD 20850

来源：

JOURNAL OF PHYSICAL CHEMISTRY A | 1997年 / 101卷 / 08期

关键词：

D O I：

10.1021/jp963817g

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

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.

引用

页码：1609 / 1618

页数：10

共 47 条

[1]

[Anonymous], 1991, Handbook of genetic algorithms

[2]

[Anonymous], 1986, NUMERICAL RECIPES C

[3] FREE-ENERGY CALCULATIONS BY COMPUTER-SIMULATION [J].