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Investigations into the Effect of Multiobjectivization in Protein Structure Prediction

  • Julia Handl
  • Simon C. Lovell
  • Joshua Knowles
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5199)

Abstract

Physics-based potential energy functions used in protein structure prediction are composed of several energy terms combined in a weighted sum. ‘Multiobjectivization’ — splitting up the energy function into its components and optimizing the components as a vector using multiobjective methods — may have beneficial effects for tackling these difficult problems. In this paper we investigate the hypotheses that multiobjectivization can (i) reduce the number of local optima in the landscapes, as seen by hillclimbers, and (ii) equalize the influence of different energy components that range over vastly different energy scales and hence usually swamp each other’s search gradients. The investigations use models of two real molecules, the alanine dipeptide and Metenkephalin under the Amber99 energy function, and consider hillclimbers with a range of mutation step sizes. Our findings support the hypotheses and also indicate that multiobjectivization is competitive with alternative methods of escaping local optima.

Keywords

Local Optimum Multiobjective Optimization Protein Structure Prediction Gaussian Mutation Alanine Dipeptide 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Julia Handl
    • 1
  • Simon C. Lovell
    • 1
  • Joshua Knowles
    • 1
  1. 1.The University of ManchesterUK

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