Representations for Evolutionary Algorithms Applied to Protein Structure Prediction Problem Using HP Model

  • Authors:
  • Paulo H. Gabriel;Alexandre C. Delbem

  • Affiliations:
  • Depto. Sistemas de Computação, ICMC/USP, São Carlos/SP, Brazil 13560-970;Depto. Sistemas de Computação, ICMC/USP, São Carlos/SP, Brazil 13560-970

  • Venue:
  • BSB '09 Proceedings of the 4th Brazilian Symposium on Bioinformatics: Advances in Bioinformatics and Computational Biology
  • Year:
  • 2009

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Abstract

Protein structure prediction (PSP) is a computational complex problem. To work with large proteins, simple protein models have been employed to represent the conformation, and evolutionary algorithms (EAs) are usually used to search for adequate solutions. However, the generation of unfeasible conformations may decrease the EA performance. For this reason, this paper presents two alternative representations that reduce the number of improper structures, improving the search process. Both representations have been investigated in terms of initial population in order to start the evolutionary process with promising regions. The results have shown a significant improvement in the fitness values (or, in other words, in solution quality).