The ant colony optimization meta-heuristic
New ideas in optimization
Ant algorithms for discrete optimization
Artificial Life
Genetic Algorithm for 3D Protein Folding Simulations
Proceedings of the 5th International Conference on Genetic Algorithms
An Ant Colony Optimization Algorithm for the 2D HP Protein Folding Problem
ANTS '02 Proceedings of the Third International Workshop on Ant Algorithms
Ants can solve constraint satisfaction problems
IEEE Transactions on Evolutionary Computation
Parallel Ant Colony Optimization for 3D Protein Structure Prediction using the HP Lattice Model
IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 6 - Volume 07
An efficient genetic algorithm for predicting protein tertiary structures in the 2D HP model
GECCO '05 Proceedings of the 7th annual conference on Genetic and evolutionary computation
Ant Algorithms: Theory and Applications
Programming and Computing Software
Review: A review of ant algorithms
Expert Systems with Applications: An International Journal
EvoCOP'05 Proceedings of the 5th European conference on Evolutionary Computation in Combinatorial Optimization
Cross-lattice behavior of general ACO folding for proteins in the HP model
Proceedings of the 28th Annual ACM Symposium on Applied Computing
Proceedings of the 15th annual conference companion on Genetic and evolutionary computation
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The prediction of a protein's structure from its amino-acid sequence is one of the most important problems in computational biology. In the current work, we focus on a widely studied abstraction of this problem, the 2-dimensional hydrophobic-polar (2D HP) protein folding problem. We present an improvedv ersion of our recently proposed Ant Colony Optimisation (ACO) algorithm for this NP-hardcom binatorial problem and demonstrate its ability to solve standard benchmark instances substantially better than the original algorithm; the performance of our new algorithm is comparable with state-of-the-art Evolutionary andMon te Carlo algorithms for this problem. The improvements over our previous ACO algorithm include long range moves that allows us to perform modification of the protein at high densities, the use of improving ants, ands elective local search. Overall, the results presented here establish our new ACO algorithm for 2D HP protein folding as a state-of-the-art methodf or this highly relevant problem from bioinformatics.