  Determining the folding core of a protein yields information about its
folding process and dynamics. The experimental procedures for identifying the
amino acids which make up the folding core include hydrogen-deuterium exchange
and $\Phi$-value analysis and can be expensive and time consuming. As such
there is a desire to improve upon existing methods for determining protein
folding cores theoretically. Here, we use a combined method of rigidity
analysis alongside coarse-grained simulations of protein motion in order to
improve folding core predictions for unbound CypA and for the CypA-CsA complex.
We find that the most specific prediction of folding cores in CypA and CypA-CsA
comes from the intersection of the results of static rigidity analysis,
implemented in the FIRST software suite, and simulations of the propensity for
flexible motion, using the FRODA tool.
