Protein folding pathways and state transitions described by classical equations of motion of an elastic network model

A dynamical approach to contact distance based protein structure determination

Protein native structure topology based folding dynamics captures many aspects of protein folding. The fact that folding is driven by a potential derived only from residue pairs in native contact, a sparse distance matrix, lead us to postulate this as a solution method to the molecular distance geometry problem. In the standard Go model non-bonded residues move under the influence of a Lennard-Jones potential and consequently folding is slow. In this study we apply a faster quadratic potential Go model to solving the full-atom distance geometry problem, where distance data is based only on residue atoms within 5 Å in the native structure. We show that the method works well when only atomic contact data is known and when a substantial proportion of this contact data is missing. Also, we show that the method can be applied in conjunction with secondary structure prediction schemes to enhance accuracy in cases of missing contact data.