A new algorithm for protein folding in the HP model
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
Tabu Search
Eighteenth national conference on Artificial intelligence
The HuGS platform: a toolkit for interactive optimization
Proceedings of the Working Conference on Advanced Visual Interfaces
Protein folding in the HP model on grid lattices with diagonals
Discrete Applied Mathematics
Stochastic protein folding simulation in the three-dimensional HP-model
Computational Biology and Chemistry
Genetic algorithms with local search optimization for protein structure prediction problem
Proceedings of the 10th annual conference on Genetic and evolutionary computation
Persistent Computations of Turing Machines
CIAA '08 Proceedings of the 13th international conference on Implementation and Applications of Automata
A Local Move Set for Protein Folding in Triangular Lattice Models
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
DFS Based Partial Pathways in GA for Protein Structure Prediction
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
Extremal Optimization for protein folding simulations on the lattice
Computers & Mathematics with Applications
Computational Biology and Chemistry
Application of tabu search strategy for finding low energy structure of protein
Artificial Intelligence in Medicine
Delta: a toolset for the structural analysis of biological sequences on a 3D triangular lattice
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Stochastic protein folding simulation in the d-dimensional HP-model
BIRD'07 Proceedings of the 1st international conference on Bioinformatics research and development
Generalized schemata theorem incorporating twin removal for protein structure prediction
PRIB'07 Proceedings of the 2nd IAPR international conference on Pattern recognition in bioinformatics
Journal of Heuristics
An on/off lattice approach to protein structure prediction from contact maps
PRIB'10 Proceedings of the 5th IAPR international conference on Pattern recognition in bioinformatics
Twin Removal in Genetic Algorithms for Protein Structure Prediction Using Low-Resolution Model
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Landscape analysis for protein-folding simulation in the h-p model
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Incorporating knowledge of secondary structures in a l-system-based encoding for protein folding
EA'05 Proceedings of the 7th international conference on Artificial Evolution
An evolutionary model based on hill-climbing search operators for protein structure prediction
EvoBIO'10 Proceedings of the 8th European conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
EvoBIO'10 Proceedings of the 8th European conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
AI'06 Proceedings of the 19th Australian joint conference on Artificial Intelligence: advances in Artificial Intelligence
A memetic approach to protein structure prediction in triangular lattices
ICONIP'11 Proceedings of the 18th international conference on Neural Information Processing - Volume Part I
Conflict resolution based global search operators for long protein structures prediction
ICONIP'11 Proceedings of the 18th international conference on Neural Information Processing - Volume Part I
On three-dimensional graph drawing and embedding
WALCOM'12 Proceedings of the 6th international conference on Algorithms and computation
Global energy minimisation and cotranslational protein folding of HP models
Journal of Global Optimization
Computational Biology and Chemistry
Hybrid evolutionary algorithm with a composite fitness function for protein structure prediction
IDEAL'12 Proceedings of the 13th international conference on Intelligent Data Engineering and Automated Learning
Memory-based local search for simplified protein structure prediction
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Random-walk: a stagnation recovery technique for simplified protein structure prediction
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
"Pull Moves” for Rectangular Lattice Polymer Models Are Not Fully Reversible
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A new genetic algorithm for simplified protein structure prediction
AI'12 Proceedings of the 25th Australasian joint conference on Advances in Artificial Intelligence
Cross-lattice behavior of general ACO folding for proteins in the HP model
Proceedings of the 28th Annual ACM Symposium on Applied Computing
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We present new lowest energy configurations for several large benchmark problems for the two-dimensional hydrophobic-hydrophilic model. We found these solutions with a generic implementation of tabu search using an apparently novel set of transformations that we call pull moves. Our experiments show that our algorithm can find these best solutions in 3 to 14 hours, on average. Pull moves appear quite effective and may also be useful for other local search algorithms for the problem. Additionally, we prove that pull moves are complete; that is, any pair of valid configurations are mutually reachable through a sequence of pull moves. Our implementation was developed with the Human-Guided Search (HuGS) middleware, which allows rapid development of interactive optimization systems.