Volume 3 Supplement 1

6th German Conference on Chemoinformatics, GCC 2010

Open Access

Confab – generation of diverse low energy conformers

Journal of Cheminformatics20113(Suppl 1):P32

DOI: 10.1186/1758-2946-3-S1-P32

Published: 19 April 2011

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

(1)
Analytical and Biological Chemistry Research Facility, University College Cork
(2)
University of Antwerp
(3)
Department of Chemistry, University of Pittsburgh

References

  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
  2. Eigen – A C++ template library for linear algebra. version 2.0. Available from http://eigen.tuxfamily.org
  3. Open Babel. version 2.3.0. Available from http://openbabel.org
  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

Copyright

© 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 (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.