Literature DB >> 1869896

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

M T Barakat1, P M Dean.   

Abstract

This paper extends an application of the method of simulated annealing for molecular matching so that the best common subsets of atom positions can be identified. Null correspondences are introduced into the difference distance matrix to enable poorly matched positions to be ignored in minimizing the objective function. The efficiency of the algorithm in finding correct subsets is rigorously tested.

Mesh：

Year:  1991        PMID： 1869896     DOI： 10.1007/bf00129750

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


  4 in total

1.  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

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

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

4.  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
  4 in total
  10 in total

1.  Maximum common subgraph isomorphism algorithms for the matching of chemical structures.

Authors:  John W Raymond; Peter Willett
Journal:  J Comput Aided Mol Des       Date:  2002-07       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.  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

5.  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

6.  The atom assignment problem in automated de novo drug design. 5. Tests for envelope-directed fragment placement based on molecular similarity.

Authors:  M T Barakat; P M Dean
Journal:  J Comput Aided Mol Des       Date:  1995-10       Impact factor: 3.686

7.  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

8.  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

9.  An exploration of a novel strategy for superposing several flexible molecules.

Authors:  T D Perkins; P M Dean
Journal:  J Comput Aided Mol Des       Date:  1993-04       Impact factor: 3.686

10.  An automated method for predicting the positions of hydrogen-bonding atoms in binding sites.

Authors:  J E Mills; T D Perkins; P M Dean
Journal:  J Comput Aided Mol Des       Date:  1997-05       Impact factor: 3.686
  10 in total

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