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Flexible ligand docking using a genetic algorithm

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Summary

Two computational techniques have been developed to explore the orientational and conformational space of a flexible ligand within an enzyme. Both methods use the Genetic Algorithm (GA) to generate conformationally flexible ligands in conjunction with algorithms from the DOCK suite of programs to characterize the receptor site. The methods are applied to three enzyme-ligand complexes: dihydrofolate reductase-methotrexate, thymidylate synthase-phenolpthalein and HIV protease-thioketal haloperidol. Conformations and orientations close to the crystallographically determined structures are obtained, as well as alternative structures with low energy. The potential for the GA method to screen a database of compounds is also examined. A collection of ligands is evaluated simultaneously, rather than docking the ligands individually into the enzyme.

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Abbreviations

GA:

genetic algorithm; dhfr, dihydrofolate reductase

mtx:

methotrexate

ts:

thymidylate synthase

fen:

phenolphalein

HIV:

human immune deficiency virus

hivp:

HIV protease

thk:

thioketal haloperidol

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Authors and Affiliations

  1. Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, 94143-0446, San Francisco, CA, U.S.A.

    C. M. Oshiro & I. D. Kuntz

  2. Department of Physical and Structural Chemsitry, SmithKline Beecham Pharmaceuticals, P.O. Box 1539, 19406-0939, King of Prussia, PA, U.S.A.

    J. Scott Dixon

Authors
  1. C. M. Oshiro
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  2. I. D. Kuntz
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  3. J. Scott Dixon
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Oshiro, C.M., Kuntz, I.D. & Dixon, J.S. Flexible ligand docking using a genetic algorithm. J Computer-Aided Mol Des 9, 113–130 (1995). https://doi.org/10.1007/BF00124402

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  • DOI: https://doi.org/10.1007/BF00124402

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