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Multispace Search For Protein Folding

  • Jun Gu
  • Bin Du
  • Panos Pardalos
Chapter
Part of the The IMA Volumes in Mathematics and its Applications book series (IMA, volume 94)

Abstract

Molecular energy minimization is one of the most challenging, unsolved problems in molecular biophysics. Due to numerous local minima in the search space, a traditional optimization method has a tendency to get stuck at some local minimum points. In this paper, for Lennard-Jones clusters, we give a multispace search algorithm for molecular energy minimization. Multispace search interplays structural operations in conjunction with the existing optimization methods. Structural operations dynamically construct a sequence of intermediate lattice structures by changing the original lattice structure. Each intermediate lattice structure is then optimized by the traditional optimization methods. Structural lattice operations disturb the environment of forming local minima, which makes multispace search a very natural approach to molecular energy minimization. We compare multispace approach with traditional optimization techniques for molecular energy minimization problems.

Key words

Molecular energy minimization optimization algorithm Lennard-Jones cluster multispace search protein folding local search 

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Copyright information

© Springer Science+Business Media New York 1997

Authors and Affiliations

  • Jun Gu
    • 1
    • 3
  • Bin Du
    • 1
    • 3
  • Panos Pardalos
    • 2
  1. 1.Department of Electrical and Computer EngineeringUniversity of CalgaryCalgaryCanada
  2. 2.Center for Applied Optimization and ISE DepartmentUniversity of FloridaGainesvilleUSA
  3. 3.Department of Computer ScienceThe Hong Kong University of Science and TechnologyKowloonHong Kong

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