An improved backtracking method for EDAs based protein folding

Benhui Chen, Long Li, Takayuki Furuzuki

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

Many Evolutionary Algorithm (EA) based methods have been proposed to solve protein structure prediction (PSP) problem in HP-lattice model. One of common difficulties of those methods is the existence of invalid individuals produced by geometrical constraints in the conformation of protein (i.e. self-avoidance in the chain). A backtracking method is often used to repair the invalid individuals of genetic search in those methods. However, there is a disadvantage in basic backtracking method, the repairing computational cost is very heavy for long sequence instances. This paper proposes an improved backtracking-based repairing method for long sequence protein folding. A detection procedure is added in backtracking method to avoid entering invalid closed areas when selecting directions for the residues. Experimental results show that the proposed method can significantly reduce the number of backtracking searching operations and the computational cost for the long protein sequences.

Original languageEnglish
Title of host publicationICCAS-SICE 2009 - ICROS-SICE International Joint Conference 2009, Proceedings
Pages4669-4674
Number of pages6
Publication statusPublished - 2009
EventICROS-SICE International Joint Conference 2009, ICCAS-SICE 2009 - Fukuoka
Duration: 2009 Aug 182009 Aug 21

Other

OtherICROS-SICE International Joint Conference 2009, ICCAS-SICE 2009
CityFukuoka
Period09/8/1809/8/21

Fingerprint

Protein folding
Proteins
Evolutionary algorithms
Conformations
Costs
Repair

Keywords

  • Backtracking
  • Estimation of Distribution Algorithms (EDAs)
  • HP model
  • Protein structure prediction (PSP)

ASJC Scopus subject areas

  • Information Systems
  • Control and Systems Engineering
  • Industrial and Manufacturing Engineering

Cite this

Chen, B., Li, L., & Furuzuki, T. (2009). An improved backtracking method for EDAs based protein folding. In ICCAS-SICE 2009 - ICROS-SICE International Joint Conference 2009, Proceedings (pp. 4669-4674). [5332962]

An improved backtracking method for EDAs based protein folding. / Chen, Benhui; Li, Long; Furuzuki, Takayuki.

ICCAS-SICE 2009 - ICROS-SICE International Joint Conference 2009, Proceedings. 2009. p. 4669-4674 5332962.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Chen, B, Li, L & Furuzuki, T 2009, An improved backtracking method for EDAs based protein folding. in ICCAS-SICE 2009 - ICROS-SICE International Joint Conference 2009, Proceedings., 5332962, pp. 4669-4674, ICROS-SICE International Joint Conference 2009, ICCAS-SICE 2009, Fukuoka, 09/8/18.
Chen B, Li L, Furuzuki T. An improved backtracking method for EDAs based protein folding. In ICCAS-SICE 2009 - ICROS-SICE International Joint Conference 2009, Proceedings. 2009. p. 4669-4674. 5332962
Chen, Benhui ; Li, Long ; Furuzuki, Takayuki. / An improved backtracking method for EDAs based protein folding. ICCAS-SICE 2009 - ICROS-SICE International Joint Conference 2009, Proceedings. 2009. pp. 4669-4674
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