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A New Genetic Algorithm for Simplified Protein Structure Prediction

  • Mahmood A. Rashid
  • Md. Tamjidul Hoque
  • M. A. Hakim Newton
  • Duc Nghia Pham
  • Abdul Sattar
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7691)

Abstract

In this paper, we present a new genetic algorithm for protein structure prediction problem using face-centred cubic lattice and hydrophobic-polar energy model. Our algorithm uses i) an exhaustive generation approach to diversify the search; ii) a novel hydrophobic core-directed macro move to intensify the search; and iii) a random-walk strategy to recover from stagnation. On a set of standard benchmark proteins, our algorithm significantly outperforms the state-of-the-art algorithms for the same models.

Keywords

Protein Structure Prediction Genetic Algorithms Local Search Lattice Models Energy Models Random-walk 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Mahmood A. Rashid
    • 1
    • 2
  • Md. Tamjidul Hoque
    • 3
  • M. A. Hakim Newton
    • 1
    • 2
  • Duc Nghia Pham
    • 1
    • 2
  • Abdul Sattar
    • 1
    • 2
  1. 1.Queensland Research LabNational ICT AustraliaAustralia
  2. 2.Institute for Integrated & Intelligent SystemsGriffith UniversityAustralia
  3. 3.Computer ScienceUniversity of New OrleansUSA

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