Mapping Protein Space Using Potentials of Mean Force

The design of novel proteins with predefined functions is a central problem of modern biosciences. Mapping the sequence-structure relations for RNAs based on secondary structures, especially the discovery of extended "neutral networks", has provided a theoretical basis for understanding the dynamics of in-vitro evolution experiments. Computer simulations have shown that the methods of evolutionary biotechnology which are based on functional RNA molecules, are feasible only because of the existence of these extended "neutral networks" in sequence space.

The main objective of our proposed research is to investigate whether similar sequence-structure relations can be found for proteins. Here we are especially interested in the question wether extended "neutral networks" exist for proteins. Whether or not a given polypeptide sequence folds into a predefined structure will be assessed by means of the potential function developed by the group of Manfred J. Sippl (CAME,Salzburg) as well as by the aprroach applied by Alan Lapedes (Los Alamos).

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