An efficient genetic algorithm for predicting protein tertiary structures in the 2D HP model

Thang Nguyen Bui, Gnanasekaran Sundarraj

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

17 Citations (Scopus)

Abstract

Given the amino acid sequence of a protein, predicting its tertiary structure is known as the protein folding problem. This problem has been widely studied under the HP model in which each amino acid is classified, based on its hydrophobicity, as an H (hydrophobic or non-polar) or a P (hydrophilic or polar). Conformation of a protein in the HP model is embedded as a self-avoiding walk in either a two-dimensional or a three-dimensional lattice. The protein folding problem in the HP model is to find a lowest energy conformation. This problem is known to be NP-hard in both two-dimensional and three-dimensional square lattices. In this paper, we present an efficient genetic algorithm for the protein folding problem under the HP model in the two-dimensional square lattice. A special feature of this algorithm is its usage of secondary structures, that the algorithm evolves, as building blocks for the conformation. Experimental results on benchmark sequences show that the algorithm performs very well against existing evolutionary algorithms and Monte Carlo algorithms.

Original languageEnglish (US)
Title of host publicationGECCO 2005 - Genetic and Evolutionary Computation Conference
EditorsH.G. Beyer, U.M. O'Reilly, D. Arnold, W. Banzhaf, C. Blum, E.W. Bonabeau, E. Cantu-Paz, D. Dasgupta, K. Deb, al et al
Pages385-392
Number of pages8
DOIs
StatePublished - Dec 1 2005
EventGECCO 2005 - Genetic and Evolutionary Computation Conference - Washington, D.C., United States
Duration: Jun 25 2005Jun 29 2005

Publication series

NameGECCO 2005 - Genetic and Evolutionary Computation Conference

Other

OtherGECCO 2005 - Genetic and Evolutionary Computation Conference
CountryUnited States
CityWashington, D.C.
Period6/25/056/29/05

Fingerprint

Protein folding
Genetic algorithms
Proteins
Conformations
Amino acids
Hydrophobicity
Evolutionary algorithms

All Science Journal Classification (ASJC) codes

  • Engineering(all)

Cite this

Bui, T. N., & Sundarraj, G. (2005). An efficient genetic algorithm for predicting protein tertiary structures in the 2D HP model. In H. G. Beyer, U. M. O'Reilly, D. Arnold, W. Banzhaf, C. Blum, E. W. Bonabeau, E. Cantu-Paz, D. Dasgupta, K. Deb, ... A. et al (Eds.), GECCO 2005 - Genetic and Evolutionary Computation Conference (pp. 385-392). (GECCO 2005 - Genetic and Evolutionary Computation Conference). https://doi.org/10.1145/1068009.1068072
Bui, Thang Nguyen ; Sundarraj, Gnanasekaran. / An efficient genetic algorithm for predicting protein tertiary structures in the 2D HP model. GECCO 2005 - Genetic and Evolutionary Computation Conference. editor / H.G. Beyer ; U.M. O'Reilly ; D. Arnold ; W. Banzhaf ; C. Blum ; E.W. Bonabeau ; E. Cantu-Paz ; D. Dasgupta ; K. Deb ; al et al. 2005. pp. 385-392 (GECCO 2005 - Genetic and Evolutionary Computation Conference).
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Bui, TN & Sundarraj, G 2005, An efficient genetic algorithm for predicting protein tertiary structures in the 2D HP model. in HG Beyer, UM O'Reilly, D Arnold, W Banzhaf, C Blum, EW Bonabeau, E Cantu-Paz, D Dasgupta, K Deb & A et al (eds), GECCO 2005 - Genetic and Evolutionary Computation Conference. GECCO 2005 - Genetic and Evolutionary Computation Conference, pp. 385-392, GECCO 2005 - Genetic and Evolutionary Computation Conference, Washington, D.C., United States, 6/25/05. https://doi.org/10.1145/1068009.1068072

An efficient genetic algorithm for predicting protein tertiary structures in the 2D HP model. / Bui, Thang Nguyen; Sundarraj, Gnanasekaran.

GECCO 2005 - Genetic and Evolutionary Computation Conference. ed. / H.G. Beyer; U.M. O'Reilly; D. Arnold; W. Banzhaf; C. Blum; E.W. Bonabeau; E. Cantu-Paz; D. Dasgupta; K. Deb; al et al. 2005. p. 385-392 (GECCO 2005 - Genetic and Evolutionary Computation Conference).

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

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Bui TN, Sundarraj G. An efficient genetic algorithm for predicting protein tertiary structures in the 2D HP model. In Beyer HG, O'Reilly UM, Arnold D, Banzhaf W, Blum C, Bonabeau EW, Cantu-Paz E, Dasgupta D, Deb K, et al A, editors, GECCO 2005 - Genetic and Evolutionary Computation Conference. 2005. p. 385-392. (GECCO 2005 - Genetic and Evolutionary Computation Conference). https://doi.org/10.1145/1068009.1068072