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Cluster analysis of molecular conformations
Author(s) -
Shenkin Peter S.,
McDonald D. Quentin
Publication year - 1994
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540150811
Subject(s) - distance matrix , cluster analysis , pairwise comparison , hierarchical clustering , computer science , cluster (spacecraft) , hierarchy , cartesian coordinate system , complete linkage clustering , visualization , matrix (chemical analysis) , distance matrices in phylogeny , data mining , mathematics , fuzzy clustering , algorithm , artificial intelligence , combinatorics , chemistry , geometry , programming language , canopy clustering algorithm , chromatography , economics , market economy
We describe a method for locating clusters of geometrically similar conformers in ensembles of chemical conformations. We first calculate the pairwise interconformational distance matrix in either torsional or Cartesian space and then use an agglomerative, single‐link clustering method to define a hierarchy of clusterings in the same space. Especially good clusterings are distinguished by high values of the separation ratio: the ratio of the shortest intercluster distance to the characteristic threshold distance defining the clustering. We also discuss other statistics. The method has been embodied in a program called XCluster, which can display the distance matrix, the hierarchy of clusterings, and the clustering statistics in a variety of formats. XCluster can also write out the clustered conformations for subsequent or simultaneous viewing with a molecular visualization program. We demonstrate the sorts of insight that this approach affords with examples obtained from conformational search and molecular dynamics procedures. © 1994 by John Wiley & Sons, Inc.