Chain growth algorithms for HP-type lattice proteins
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
Future Generation Computer Systems
A complete and effective move set for simplified protein folding
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Ant Colony Optimization
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 improved ant colony optimisation algorithm for the 2D HP protein folding problem
AI'03 Proceedings of the 16th Canadian society for computational studies of intelligence conference on Advances in artificial intelligence
Twin Removal in Genetic Algorithms for Protein Structure Prediction Using Low-Resolution Model
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On Lattice Protein Structure Prediction Revisited
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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The computational investigation of protein folding is one of the most relevant challenges in bioinformatics. In this field, simplified lattice models for proteins like the classical HP model have been proposed, and different lattice types can be employed. A promising approach to find ground state conformations relies on Ant Colony Optimization (ACO), a popular biology-inspired heuristics: several variants have been implemented so far, on square lattices in 2D and 3D. In this paper we propose a general scheme of ACO for HP on both square and triangular lattices in 2D and 3D, including also a novel initialization procedure for the pheromone matrix according to some pre-computed suboptimal conformations. The algorithm behavior, considering the influence of the optional parts and the required parameter tuning, is investigated for the first time with experiments that systematically span different lattice types. The test outcomes are useful in understanding how to operate on the algorithm parameters. The presented results are used to sketch out general guidelines for the practical employment of ACO in conformational studies, depending on the chosen sequences and lattice types.