confab – generation of diverse low energy conformers
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POSTER PRESENTATION Open Access
Confab–generation of diverse low energyconformersNM O’Boyle1*, T Vandermeersch2, GR Hutchison3
From 6th German Conference on Chemoinformatics, GCC 2010Goslar, Germany. 7-9 November 2010
We present a new program for conformer generation,Confab, which aims to generate diverse low energy con-formers that span the space of all possible conforma-tions. Such conformers are required for use in fieldssuch as docking and pharmacophore searching andgeneration.Confab uses a torsion driving approach to travel
through the set of systematically generated conformersselecting those which are below a particular energy cut-off and which are structurally distinct (according to auser-specified RMSD) from those conformers alreadyselected. The RMSD is evaluated using Kabsch align-ment [1] of heavy atoms and takes symmetry intoaccount. To improve performance, the alignment is car-ried out using the Eigen maths library [2], an opensource library with an emphasis on speed and efficiency.In addition, the initial pass through the set of confor-mers uses a tree data structure to minimise the numberof alignments required to identify a structure as similarto a previous one.Confab is open source, and uses the Open Babel che-
minformatics toolkit [3,4].
Author details1Analytical and Biological Chemistry Research Facility, University CollegeCork, Cork, Ireland. 2University of Antwerp, Antwerp, Belgium. 3Departmentof Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh,Pennsylvania 15260, USA.
Published: 19 April 2011
References1. Kabsch W: A solution of the best rotation to relate two sets of vectors.
Acta Cryst. A. 1976, 32:922-923.
2. Eigen – A C++ template library for linear algebra. , version 2.0. Availablefrom 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 ChemicalInformatics. J Chem Inf Model 2006, 46:991-998.
doi:10.1186/1758-2946-3-S1-P32Cite this article as: O’Boyle et al.: Confab–generation of diverse lowenergy conformers. Journal of Cheminformatics 2011 3(Suppl 1):P32.
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* Correspondence: [email protected] and Biological Chemistry Research Facility, University CollegeCork, Cork, IrelandFull list of author information is available at the end of the article
O’Boyle et al. Journal of Cheminformatics 2011, 3(Suppl 1):P32http://www.jcheminf.com/content/3/S1/P32
© 2011 O’Boyle et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative CommonsAttribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction inany medium, provided the original work is properly cited.