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Journal of Cheminformatics

, 3:P32 | Cite as

Confab – generation of diverse low energy conformers

Open Access
Poster presentation

Keywords

Data Structure Open Source Tree Data Heavy Atom Energy Cutoff 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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].

References

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

Copyright information

© 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.

Authors and Affiliations

  1. 1.Analytical and Biological Chemistry Research FacilityUniversity College CorkCorkIreland
  2. 2.University of AntwerpAntwerpBelgium
  3. 3.Department of ChemistryUniversity of PittsburghPittsburghUSA

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