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  • Poster presentation
  • Open Access

Confab – generation of diverse low energy conformers

Journal of Cheminformatics20113 (Suppl 1) :P32

  • Published:


  • Data Structure
  • Open Source
  • Tree Data
  • Heavy Atom
  • Energy Cutoff

We present a new program for conformer generation, Confab, which aims to generate diverse low energy conformers that span the space of all possible conformations. Such conformers are required for use in fields such as docking and pharmacophore searching and generation.

Confab uses a torsion driving approach to travel through the set of systematically generated conformers selecting those which are below a particular energy cutoff and which are structurally distinct (according to a user-specified RMSD) from those conformers already selected. The RMSD is evaluated using Kabsch alignment [1] of heavy atoms and takes symmetry into account. To improve performance, the alignment is carried out using the Eigen maths library [2], an open source library with an emphasis on speed and efficiency. In addition, the initial pass through the set of conformers uses a tree data structure to minimise the number of alignments required to identify a structure as similar to a previous one.

Confab is open source, and uses the Open Babel cheminformatics toolkit [3, 4].

Authors’ Affiliations

Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland
University of Antwerp, Antwerp, Belgium
Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA


  1. Kabsch W: A solution of the best rotation to relate two sets of vectors. Acta Cryst. A. 1976, 32: 922-923. 10.1107/S0567739476001873.View ArticleGoogle Scholar
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  3. Open Babel. version 2.3.0. Available from
  4. Guha R, Howard MT, Hutchison GR, Murray-Rust P, Rzepa H, Steinbeck C, Wegner JK, Willighagen E: The Blue Obelisk – Interoperability in Chemical Informatics. J Chem Inf Model. 2006, 46: 991-998. 10.1021/ci050400b.View ArticleGoogle Scholar


© O’Boyle et al; licensee BioMed Central Ltd. 2011

This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.