Using simplified protein representation as a reference potential for all-atom calculations of folding free energy

An effective approach for evaluating folding free-energy surfaces of explicit all-atom models is developed and examined. This approach is based on using the potential of a simplified protein model as a reference potential for calculating the free energy of the corresponding explicit model. Preliminary results are presented for the folding free energy of a 12-residue helix. The potential of the method for studies of protein-folding processes is discussed, emphasizing the ability to determine the difference between the results of simplified and explicit models. This can help in establishing the validity of simplified folding models.