CLUSTER-ANALYSIS OF MOLECULAR-CONFORMATIONS

We describe a method for locating clusters of geometrically similar co nformers in ensembles of chemical conformations. We first calculate th e 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. Especia lly good clusterings are distinguished by high values of the separatio n ratio: the ratio of the shortest intercluster distance to the charac teristic threshold distance defining the clustering. We also discuss o ther statistics. The method has been embodied in a program called XClu ster, which can display the distance matrix, the hierarchy of clusteri ngs, and the clustering statistics in a variety of formats. XCluster c an also write out the clustered conformations for subsequent or simult aneous 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. (C) 199 4 by John Wiley and Sons, Inc.