Chain growth algorithms for HP-type lattice proteins
RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
On the complexity of protein folding (extended abstract)
STOC '98 Proceedings of the thirtieth annual ACM symposium on Theory of computing
Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
Excluding Symmetries in Constraint-Based Search
CP '99 Proceedings of the 5th International Conference on Principles and Practice of Constraint Programming
Optimally Compact Finite Sphere Packings - Hydrophobic Cores in the FCC
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
The algorithmics of folding proteins on lattices
Discrete Applied Mathematics - Special issue: Computational molecular biology series issue IV
Heuristics, optimizations, and parallelism for protein structure prediction in CLP(FD)
PPDP '05 Proceedings of the 7th ACM SIGPLAN international conference on Principles and practice of declarative programming
A constraint logic programming approach to 3D structure determination of large protein complexes
Proceedings of the 2006 ACM symposium on Applied computing
International Journal of Data Mining and Bioinformatics
Agent-based protein structure prediction
Multiagent and Grid Systems - Multi-agent systems for medicine, computational biology, and bioinformatics
Protein Structure Prediction with Large Neighborhood Constraint Programming Search
CP '08 Proceedings of the 14th international conference on Principles and Practice of Constraint Programming
An Improved Population Migration Algorithm for the Prediction of Protein Folding
ISNN 2009 Proceedings of the 6th International Symposium on Neural Networks: Advances in Neural Networks - Part III
Logic Programming Techniques in Protein Structure Determination: Methodologies and Results
LPNMR '09 Proceedings of the 10th International Conference on Logic Programming and Nonmonotonic Reasoning
International Journal of Data Mining and Bioinformatics
On Lattice Protein Structure Prediction Revisited
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A new constraint solver for 3d lattices and its application to the protein folding problem
LPAR'05 Proceedings of the 12th international conference on Logic for Programming, Artificial Intelligence, and Reasoning
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The protein structure prediction problem is one of the most (if not ithe most) important problem in computational biology. This problem consists of finding the conformation of a protein with minimal energy. Because of the complexity of this problem, simplified models like Dill's HP-lattice model [15], [16] have become a major tool for investigating general properties of protein folding. Even for this simplified model, the structure prediction problem has been shown to be NP-complete [5], [7]. We describe a constraint formulation of the HP-model structure prediction problem, and present the basic constraints and search strategy. Of course, the simple formulation would not lead to an efficient algorithm. We therefore describe redundant constraints to prune the search tree. Furthermore, we need bounding function for the energy of an HP-protein. We introduce a new lower bound based on partial knowledge about the final conformation (namely the distribution of H-monomers to layers).