Efficiency of tabu-search-based conformational search algorithms

Authors

  • Christoph Grebner,

    1. Julius-Maximilians-Universität Würzburg, Institut für Physikalische und Theoretische Chemie, Am Hubland, 97074 Würzburg, Germany
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  • Johannes Becker,

    1. Julius-Maximilians-Universität Würzburg, Institut für Physikalische und Theoretische Chemie, Am Hubland, 97074 Würzburg, Germany
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  • Svetlana Stepanenko,

    1. Julius-Maximilians-Universität Würzburg, Institut für Physikalische und Theoretische Chemie, Am Hubland, 97074 Würzburg, Germany
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  • Bernd Engels

    Corresponding author
    1. Julius-Maximilians-Universität Würzburg, Institut für Physikalische und Theoretische Chemie, Am Hubland, 97074 Würzburg, Germany
    • Julius-Maximilians-Universität Würzburg, Institut für Physikalische und Theoretische Chemie, Am Hubland, 97074 Würzburg, Germany
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Abstract

Efficient conformational search or sampling approaches play an integral role in molecular modeling, leading to a strong demand for even faster and more reliable conformer search algorithms. This article compares the efficiency of a molecular dynamics method, a simulated annealing method, and the basin hopping (BH) approach (which are widely used in this field) with a previously suggested tabu-search-based approach called gradient only tabu search (GOTS). The study emphasizes the success of the GOTS procedure and, more importantly, shows that an approach which combines BH and GOTS outperforms the single methods in efficiency and speed. We also show that ring structures built by a hydrogen bond are useful as starting points for conformational search investigations of peptides and organic ligands with biological activities, especially in structures that contain multiple rings. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

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