TY - JOUR

T1 - Protein structure prediction using bee colony optimization metaheuristic

AU - Fonseca, Rasmus

AU - Paluszewski, Martin

AU - Winter, Pawel

PY - 2010

Y1 - 2010

N2 - Predicting the native structure of proteins is one of the most challenging problems in molecular biology. The goal is to determine the three-dimensional struc- ture from the one-dimensional amino acid sequence. De novo prediction algorithms seek to do this by developing a representation of the proteins structure, an energy potential and some optimization algorithm that ¿nds the structure with minimal energy.Bee Colony Optimization (BCO) is a relatively new approach to solving opti- mization problems based on the foraging behaviour of bees. Several variants of BCO have been suggested in the literature. We have devised a new variant that uni¿es the existing and is much more ¿exible with respect to replacing the various elements of the BCO. In particular this applies to the choice of the local search as well as the method for generating scout locations and performing the waggle dance. We apply our BCO method to generate good solutions to the protein structure prediction problem. The results show that BCO generally ¿nds better solutions than simulated annealing which so far has been the metaheuristic of choice for this problem.

AB - Predicting the native structure of proteins is one of the most challenging problems in molecular biology. The goal is to determine the three-dimensional struc- ture from the one-dimensional amino acid sequence. De novo prediction algorithms seek to do this by developing a representation of the proteins structure, an energy potential and some optimization algorithm that ¿nds the structure with minimal energy.Bee Colony Optimization (BCO) is a relatively new approach to solving opti- mization problems based on the foraging behaviour of bees. Several variants of BCO have been suggested in the literature. We have devised a new variant that uni¿es the existing and is much more ¿exible with respect to replacing the various elements of the BCO. In particular this applies to the choice of the local search as well as the method for generating scout locations and performing the waggle dance. We apply our BCO method to generate good solutions to the protein structure prediction problem. The results show that BCO generally ¿nds better solutions than simulated annealing which so far has been the metaheuristic of choice for this problem.

KW - Faculty of Science

KW - Protein Struktur Forudsigelse

KW - Bee Colony Optimization

KW - Metaheuristik

KW - Protein Structure Prediction

KW - Bee Colony Optimization

KW - Metaheuristic

U2 - 10.1007/s10852-010-9125-1

DO - 10.1007/s10852-010-9125-1

M3 - Journal article

VL - 9

SP - 181

EP - 194

JO - Journal of Mathematical Modelling and Algorithms in Operations Research

JF - Journal of Mathematical Modelling and Algorithms in Operations Research

SN - 2214-2487

IS - 2

ER -