Journal of Computer-Aided Molecular Design

, Volume 23, Issue 1, pp 1–12 | Cite as

An improved adaptive genetic algorithm for protein–ligand docking

  • Ling Kang
  • Honglin Li
  • Hualiang Jiang
  • Xicheng Wang


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.


Genetic algorithms Information entropy Molecular docking Optimization design Penalty function Self-adaptation 



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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Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Ling Kang
    • 1
    • 2
  • Honglin Li
    • 2
    • 3
  • Hualiang Jiang
    • 3
  • Xicheng Wang
    • 2
  1. 1.Department of Computer Science and Engineering, School of Electronic and Information EngineeringDalian University of TechnologyDalianChina
  2. 2.Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial EquipmentDalian University of TechnologyDalianChina
  3. 3.Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina

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