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

  • Ling Kang
  • Honglin Li
  • Xiaoyu Zhao
  • Hualiang JiangEmail author
  • Xicheng WangEmail author
Original Paper

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.

Keywords

Information entropy Genetic algorithm Molecular docking Multi-scale optimization model Residue groups 

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Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  1. 1.Department of Computer Science and Engineering, School of Electronic and Information EngineeringDalian University of TechnologyDalianPeople’s Republic of China
  2. 2.Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial EquipmentDalian University of TechnologyDalianPeople’s Republic of China
  3. 3.Drug Discovery and Design Center, State Key Laboratory of Drug ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiPeople’s Republic of China

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