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An improved adaptive genetic algorithm for protein–ligand docking

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Abstract

A new optimization model of molecular docking is proposed, and a fast flexible docking method based on an improved adaptive genetic algorithm is developed in this paper. The algorithm takes some advanced techniques, such as multi-population genetic strategy, entropy-based searching technique with self-adaptation and the quasi-exact penalty. A new iteration scheme in conjunction with above techniques is employed to speed up the optimization process and to ensure very rapid and steady convergence. The docking accuracy and efficiency of the method are evaluated by docking results from GOLD test data set, which contains 134 protein–ligand complexes. In over 66.2% of the complexes, the docked pose was within 2.0 Å root-mean-square deviation (RMSD) of the X-ray structure. Docking time is approximately in proportion to the number of the rotatable bonds of ligands.

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Acknowledgements

The authors gratefully acknowledge financial support for this work from the National Natural Science Foundation (No. 10772042), the Subsidized by the Special Funds for Major State Basic Research Project (No. 2004CB518901) and High Science and Technology Project (No. 2006AA01A124) of China.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, School of Electronic and Information Engineering, Dalian University of Technology, Dalian, 116023, China

    Ling Kang

  2. Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology, Dalian, 116023, China

    Ling Kang, Honglin Li & Xicheng Wang

  3. Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China

    Honglin Li & Hualiang Jiang

Authors
  1. Ling Kang
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  2. Honglin Li
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  3. Hualiang Jiang
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  4. Xicheng Wang
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Corresponding author

Correspondence to Xicheng Wang.

Additional information

Ling Kang and Honglin Li have contributed equally to this work.

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Kang, L., Li, H., Jiang, H. et al. An improved adaptive genetic algorithm for protein–ligand docking. J Comput Aided Mol Des 23, 1–12 (2009). https://doi.org/10.1007/s10822-008-9232-5

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  • DOI: https://doi.org/10.1007/s10822-008-9232-5

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