Genetic algorithms for protein tertiary structure prediction

A genetic algorithm is used to search energetically and structurally favorable conformations. We use a hybrid protein representation, three operators to manipulate the protein 'genes', and a fitness function based on a simple force field. The prototype was applied to the ab initio prediction of Crambin. None of the conformations generated with a non-biased fitness function are similar to the native conformation but all of them show a much better overall fitness than the native structure. If guided by r.m.s. deviation the native conformation was reproduced at 1.3 AA. Therefore, the genetic algorithm's search was successful but the fitness function was no good indicator for native structure. In a side chain placement experiment Crambin was reproduced at 1.86 AA r.m.s. deviation.<
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