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Molecular structure matching by simulated annealing. I. A comparison between different cooling schedules.

作者信息

Barakat M T, Dean P M

机构信息

Department of Pharmacology, University of Cambridge, U.K.

出版信息

J Comput Aided Mol Des. 1990 Sep;4(3):295-316. doi: 10.1007/BF00125017.

DOI:10.1007/BF00125017
PMID:2280266
Abstract

This paper outlines an application of the theory of simulated annealing to molecular matching problems. Three cooling schedules are examined: linear, exponential and dynamic cooling. The objective function is the sum of the elements of the difference distance matrix between the two molecules generated by continual reordering of one molecule. Extensive tests of the algorithms have been performed on random coordinate data together with two related protein structures. Combinatorial problems, inherent in the assignment of atom correspondences, are effectively overcome by simulated annealing. The algorithms outlined here can readily optimize molecular matching problems with 150 atoms.

摘要

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本文引用的文献

1
Optimization by simulated annealing.模拟退火优化。
Science. 1983 May 13;220(4598):671-80. doi: 10.1126/science.220.4598.671.
2
Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.大肠杆菌和干酪乳杆菌二氢叶酸还原酶的晶体结构在1.7埃分辨率下的精修。I. 甲氨蝶呤的一般特征和结合情况
J Biol Chem. 1982 Nov 25;257(22):13650-62.
3
The search for functional correspondences in molecular structure between two dissimilar molecules.寻找两个不同分子之间分子结构中的功能对应关系。
J Comput Aided Mol Des. 1997 May;11(3):229-42. doi: 10.1023/a:1007900527102.
4
Molecular surface-volume and property matching to superpose flexible dissimilar molecules.分子表面体积和性质匹配以叠加柔性不同分子。
J Comput Aided Mol Des. 1995 Dec;9(6):479-90. doi: 10.1007/BF00124319.
5
The atom assignment problem in automated de novo drug design. 3. Algorithms for optimization of fragment placement onto 3D molecular graphs.
J Comput Aided Mol Des. 1995 Aug;9(4):359-72. doi: 10.1007/BF00125177.
6
The use of an algorithmic method for small molecule superimpositions in the design of antiviral agents.
J Comput Aided Mol Des. 1993 Jun;7(3):325-35. doi: 10.1007/BF00125506.
7
An exploration of a novel strategy for superposing several flexible molecules.一种叠加多个柔性分子的新策略的探索。
J Comput Aided Mol Des. 1993 Apr;7(2):155-72. doi: 10.1007/BF00126442.
8
A Monte Carlo pharmacophore generation procedure: application to the human PAF receptor.
J Comput Aided Mol Des. 1993 Oct;7(5):515-34. doi: 10.1007/BF00124360.
9
Molecular structure matching by simulated annealing. II. An exploration of the evolution of configuration landscape problems.
J Comput Aided Mol Des. 1990 Sep;4(3):317-30. doi: 10.1007/BF00125018.
10
Molecular structure matching by simulated annealing. III. The incorporation of null correspondences into the matching problem.通过模拟退火进行分子结构匹配。III. 将空对应关系纳入匹配问题。
J Comput Aided Mol Des. 1991 Apr;5(2):107-17. doi: 10.1007/BF00129750.
J Theor Biol. 1985 Sep 21;116(2):215-24. doi: 10.1016/s0022-5193(85)80265-4.
4
Crystallographic refinement by simulated annealing. Application to a 2.8 A resolution structure of aspartate aminotransferase.通过模拟退火进行晶体学精修。应用于天冬氨酸转氨酶2.8埃分辨率结构。
J Mol Biol. 1988 Oct 5;203(3):803-16. doi: 10.1016/0022-2836(88)90211-2.
5
The alignment of protein structures in three dimensions.蛋白质结构的三维比对。
Bull Math Biol. 1989;51(1):55-78. doi: 10.1007/BF02458836.
6
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J Comput Aided Mol Des. 1990 Sep;4(3):317-30. doi: 10.1007/BF00125018.
7
A simplified representation of protein conformations for rapid simulation of protein folding.一种用于蛋白质折叠快速模拟的蛋白质构象简化表示法。
J Mol Biol. 1976 Jun 14;104(1):59-107. doi: 10.1016/0022-2836(76)90004-8.