Literature DB >> 2280266

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

M T Barakat1, P M Dean.   

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.

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Year:  1990        PMID： 2280266     DOI： 10.1007/bf00125017

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN： 0920-654X            Impact factor:   3.686


  7 in total

1.  Optimization by simulated annealing.

Authors:  S Kirkpatrick; C D Gelatt; M P Vecchi
Journal:  Science       Date:  1983-05-13       Impact factor: 47.728

2.  Molecular structure matching by simulated annealing. II. An exploration of the evolution of configuration landscape problems.

Authors:  M T Barakat; P M Dean
Journal:  J Comput Aided Mol Des       Date:  1990-09       Impact factor: 3.686

3.  A simplified representation of protein conformations for rapid simulation of protein folding.

Authors:  M Levitt
Journal:  J Mol Biol       Date:  1976-06-14       Impact factor: 5.469

4.  Crystallographic refinement by simulated annealing. Application to a 2.8 A resolution structure of aspartate aminotransferase.

Authors:  A T Brünger
Journal:  J Mol Biol       Date:  1988-10-05       Impact factor: 5.469

5.  The alignment of protein structures in three dimensions.

Authors:  M Zuker; R L Somorjai
Journal:  Bull Math Biol       Date:  1989       Impact factor: 1.758

6.  The search for functional correspondences in molecular structure between two dissimilar molecules.

Authors:  D J Danziger; P M Dean
Journal:  J Theor Biol       Date:  1985-09-21       Impact factor: 2.691

7.  Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.

Authors:  J T Bolin; D J Filman; D A Matthews; R C Hamlin; J Kraut
Journal:  J Biol Chem       Date:  1982-11-25       Impact factor: 5.157
  7 in total
  13 in total

1.  SLATE: a method for the superposition of flexible ligands.

Authors:  J E Mills; I J de Esch; T D Perkins; P M Dean
Journal:  J Comput Aided Mol Des       Date:  2001-01       Impact factor: 3.686

2.  Automatic superposition of drug molecules based on their common receptor site.

Authors:  Y Kato; A Inoue; M Yamada; N Tomioka; A Itai
Journal:  J Comput Aided Mol Des       Date:  1992-10       Impact factor: 3.686

3.  Molecular structure matching by simulated annealing. IV. Classification of atom correspondences in sets of dissimilar molecules.

Authors:  M C Papadopoulos; P M Dean
Journal:  J Comput Aided Mol Des       Date:  1991-04       Impact factor: 3.686

4.  Molecular structure matching by simulated annealing. III. The incorporation of null correspondences into the matching problem.

Authors:  M T Barakat; P M Dean
Journal:  J Comput Aided Mol Des       Date:  1991-04       Impact factor: 3.686

5.  A fast and efficient method for 2D and 3D molecular shape description.

Authors:  G W Bemis; I D Kuntz
Journal:  J Comput Aided Mol Des       Date:  1992-12       Impact factor: 3.686

6.  Molecular structure matching by simulated annealing. II. An exploration of the evolution of configuration landscape problems.

Authors:  M T Barakat; P M Dean
Journal:  J Comput Aided Mol Des       Date:  1990-09       Impact factor: 3.686

7.  Molecular surface-volume and property matching to superpose flexible dissimilar molecules.

Authors:  T D Perkins; J E Mills; P M Dean
Journal:  J Comput Aided Mol Des       Date:  1995-12       Impact factor: 3.686

8.  The use of an algorithmic method for small molecule superimpositions in the design of antiviral agents.

Authors:  G Diana; E P Jaeger; M L Peterson; A M Treasurywala
Journal:  J Comput Aided Mol Des       Date:  1993-06       Impact factor: 3.686

9.  The atom assignment problem in automated de novo drug design. 3. Algorithms for optimization of fragment placement onto 3D molecular graphs.

Authors:  M T Barakat; P M Dean
Journal:  J Comput Aided Mol Des       Date:  1995-08       Impact factor: 3.686

10.  A Monte Carlo pharmacophore generation procedure: application to the human PAF receptor.

Authors:  E E Hodgkin; A Miller; M Whittaker
Journal:  J Comput Aided Mol Des       Date:  1993-10       Impact factor: 3.686
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