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
An Upper Bound for Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC)
COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
Fast, Constraint-Based Threading of HP-Sequences to Hydrophobic Cores
CP '01 Proceedings of the 7th International Conference on Principles and Practice of Constraint Programming
Long proteins with unique optimal foldings in the H-P model
Computational Geometry: Theory and Applications - Special issue: The European workshop on computational geometry -- CG01
AI'06 Proceedings of the 19th Australian joint conference on Artificial Intelligence: advances in Artificial Intelligence
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Lattice protein models are used for hierarchical approaches to protein structure prediction, as well as for investigating principles of protein folding. The problem is that there is so far no known lattice that can model real protein conformations with good quality, and for which there is an efficient method to prove whether a conformation found by some heuristic algorithm is optimal. We present such a method for the FCC-HP-Model [3]. For the FCC-HP-Model, we need to find conformations with a maximally compact hydrophobic core. Our method allows us to enumerate maximally compact hydrophobic cores for sufficiently great number of hydrophobic amino-acids. We have used our method to prove the optimality of heuristically predicted structures for HP-sequences in the FCC-HP-model.