Here we highlight our recent studies which showed that simulation of protein folding process, with the use of knowledge-based potentials and reduced representation of the polypeptide chain, can be a useful method in prediction of experimental Phi values. Apart from providing hints for experimental design, the simulation method (by delivering trajectory of conformations) enables interpretation of the Phi values. The interpretation is a non-trivial task, especially as the obtaining of reliable Phi values is not-trivial either. Here, we present a protein chain mobility profile, from simulation of B domain of protein A, consistent with a detailed Phi value analysis.
