Protein molecular evolution protocols

To validate the molecular evolution protocols to be presented, a model that relates amino acid sequence to protein function is needed. Of course, the real test of these protocols should be experimental, and I hope that these experiments will be forthcoming. To stimulate interest in the proposed protocols, their effectiveness will be simulated on a model of protein function. Such a model would seem to be difficult to construct. It is extremely difficult to determine the three-dimensional structure of a protein given the amino acid sequence. Moreover, it is extremely difficult to calculate any of the typical figures of merit given the three-dimensional structure of a protein. 

In the simulated molecular evolutions, the experiment is continued for 100 rounds. Tliis is a relatively large number of rounds to carry out experimentally. With the most powerful protocols, however, it is possible to evolve proteins ab initio. This feat has not been achieved to date in the laboratory. To mimic this feat of Nature, one should be willing to do some number of rounds. 

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