Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
The algorithmics of folding proteins on lattices
Discrete Applied Mathematics - Special issue: Computational molecular biology series issue IV
Dynamic Programming
Inverse protein folding on 2D off-lattice model: initial results and perspectives
EvoBIO'07 Proceedings of the 5th European conference on Evolutionary computation, machine learning and data mining in bioinformatics
Protein Folding in Simplified Models With Estimation of Distribution Algorithms
IEEE Transactions on Evolutionary Computation
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An approach to the inverse protein folding problem is described which combines a simulated annealing algorithm with template matching using the Bellman criteria. Solutions to proposed target structures are found by iteratively constructing the most similar solution. The folding model is based upon the traditional 2D HP protein lattice with a modified Viterbi dynamic programming algorithm. Initial results of both the optimal folding problem and the inverse protein problem are presented.