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A novel conformation optimization model and algorithm for structure-based drug design

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Abstract

In this paper, we present a multi-scale optimization model and an entropy-based genetic algorithm for molecular docking. In this model, we introduce to the refined docking design a concept of residue groups based on induced-fit and adopt a combination of conformations in different scales. A new iteration scheme, in conjunction with multi-population evolution strategy, entropy-based searching technique with narrowing down space and the quasi-exact penalty function, is developed to address the optimization problem for molecular docking. A new docking program that accounts for protein flexibility has also been developed. The docking results indicate that the method can be efficiently employed in structure-based drug design.

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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, People’s Republic of China

    Ling Kang

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

    Ling Kang, Honglin Li, Xiaoyu Zhao & 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, People’s Republic of China

    Honglin Li & Hualiang Jiang

Authors
  1. Ling Kang
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  2. Honglin Li
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  3. Xiaoyu Zhao
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  4. Hualiang Jiang
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  5. Xicheng Wang
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Corresponding authors

Correspondence to Hualiang Jiang or Xicheng Wang.

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Kang, L., Li, H., Zhao, X. et al. A novel conformation optimization model and algorithm for structure-based drug design. J Math Chem 46, 182–198 (2009). https://doi.org/10.1007/s10910-008-9454-8

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  • DOI: https://doi.org/10.1007/s10910-008-9454-8

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