MOLECULAR-STRUCTURE MATCHING BY SIMULATED ANNEALING .1. A COMPARISON BETWEEN DIFFERENT COOLING SCHEDULES

被引：44

作者：

BARAKAT, MT

DEAN, PM

机构：

[1] Department of Pharmacology, University of Cambridge, Cambridge, CB2 1QJ, Tennis Court Road

来源：

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN | 1990年 / 4卷 / 03期

关键词：

Molecular matching; Molecular similarity; Simulated annealing;

D O I：

10.1007/BF00125017

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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. © 1990 ESCOM Science Publishers B.V.

引用

页码：295 / 316

页数：22

共 26 条

[1]

Willett P., Similarity and Clustering in Chemical Information Systems, (1987)

[2]

Dean P.M., Concepts and Applications of Molecular Similarity, (1990)

[3]

Danziger D.J., Dean P.M., J. Theor. Biol., 116, (1985)

[4]

Dean P.M., Callow P., Chau P.-L., J. Mol. Graph., 6, (1988)

[5]

Bowen-Jenkins P.E., Cooper D.L., Richards W.G., J. Phys. Chem., 89, (1985)

[6]

Maggiora G., Johnson M., Concepts and Applications of Molecular Similarity, (1990)

[7]

Sedgewick R., Algorithms, (1984)

[8]

Kirkpatrick S., Gelatt C.D., Vecchi M.P., Science, 220, (1983)

[9]

Metropolis N., Rosenbluth A., Rosenbluth M., Teller A., Teller E., J. Chem. Physics, 21, (1953)

[10]

Kirkpatrick S., Toulouse G., Configuration space analysis of travelling salesman problems, Journal de Physique, 46, (1985)

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