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

A set of 6 molecules, active at the benzodiazepine GABAA site are matched pairwise with one member of the set in turn. Matchings are performed by simulated annealing using null correspondences to reject poorly matched atom positions. Cluster analysis is employed to identify molecular similarities after an optimal molecular superimposition has been discovered. A statistic for the compactness of clustered atom positions is suggested. The introduction of null correspondences causes the clusters of matched atoms to become more compact.