  We present a new method that enables the identification and analysis of both
transition and metastable conformational states from atomistic or
coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented
and studied by using both analytical and actual examples from MD simulations of
the helix-forming peptide Ala5, and of a larger system, the epidermal growth
factor receptor (EGFR) protein. In all cases, our method identifies
automatically the corresponding transition states and metastable conformations
in an optimal way, with the input of a set of relevant coordinates, by
capturing accurately the intrinsic slowest relaxation rate. Our approach
provides a general and easy to implement analysis method that provides unique
insight into the molecular mechanism and the rare but crucial rate limiting
conformational pathways occurring in complex dynamical systems such as
molecular trajectories.
