WHAT IF: A molecular modeling and drug design program
Journal of Molecular Graphics
Evolutionary algorithms in theory and practice: evolution strategies, evolutionary programming, genetic algorithms
Multi-Objective Optimization Using Evolutionary Algorithms
Multi-Objective Optimization Using Evolutionary Algorithms
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The prediction of the native structures of proteins, the so-called protein folding problem, is a NP hard multi-minima optimization problem for which to date no routine solutions exist. Using an evolutionary approach we have addressed a problem that is related to protein folding though much simpler: the computational improvement of small proteins or peptides with respect to stability and biological function. The solution of this problem is relevant for the life sciences, e.g. because it would help to optimize peptide drugs.In a first experiment we used the proposed algorithm to stabilize a previously destabilized mutant of the otherwise stable folding Villin Headpiece. The algorithm generated amongst others a sequence that reverted the destabilizing mutation and introduced a second mutation. In terms of the used model this second mutation resulted in a more stable peptide than the original Villin Headpiece.