This application allows one to generate an unfolded state ensemble using a self-avoiding statistical coil model that is based on backbone conformational preferences from a coil library, a subset of protein data bank.

The model reproduces two apparently contradicting behaviors observed in the chemically denatured state of a variety of proteins: random coiling scaling of the radius of gyration and the presence of significant amounts local backbone structure (NMR residual dipolar couplings, RDCs).  The agreement with the NMR data substantially improves when the backbone conformational preferences include correlations arising from the chemical and conformational identity of neighboring residues. Although the unfolded ensembles match the experimental observables, they do not display evidence of native-like topology. By providing an accurate representation of the unfolded state, our statistical coil model can be used to improve thermodynamic and kinetic modeling of protein folding. To read more about our statistical coil model for the unfolded state published in [download pdf] PNAS 2005 .

Credits and Acknowledgment