Conformer clustering algorithm and its application for crown-type macrocycles

B. Vesterman, V. Golender, L. Golender, B. Fuchs*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


An efficient conformer clustering algorithm designed for treating molecular modeling problems of flexible molecules associated with a large variety of conformers is described. It incorporates a fast algorithm for the generation of chemical graph automorphisms allowing to easily discard equivalent conformers for symmetrical structures. The cluster is defined as a set of conformers deviating from the "central conformer" less than the allowed threshold. The deviation is calculated as a maximum distance between the matched atoms. Matched atoms can include all heavy atoms that can be superimposed according to graph automorphism mappings or a special subset of atoms indicated by the user. Using the "central conformer" as a meaningful representative of a cluster significantly reduces molecular modeling efforts without losing the features of the system. Application of the algorithm to the ion recognition study of the newly synthesized macrocyclic host is presented.

Original languageEnglish
Pages (from-to)145-151
Number of pages7
JournalJournal of Molecular Structure: THEOCHEM
Issue number1-3 SPEC. ISS.
StatePublished - 27 Sep 1996


  • Chemical graph
  • Cluster-analysis
  • Conformational space
  • Conformer clustering
  • Host-guest interaction
  • Ion recognition
  • Macrocycle
  • Molecular modeling


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