Estimate the per-residue entropy loss upon folding of an input pdb structure.
The Calculation uses the following secondary structure assignment according to DSSP*:
Helix - alpha, 310, or Pi helix
Sheet - extended structure
Typical Coil along with Turn regions as defined by DSSP
[residue] [amino acid] [secondary structure] [# of sidechain rotamers] [backbone entropy loss] [sidechain entropy loss] [total entropy loss]
There is no residual structure in the denatured state. If there is residual structure, one could submit a second model with the residual structure and take the difference between the two.
Any regions that are unfolded-like in the structure (e.g. long unstructured loops) will be overestimated in the loss of backbone entropy. Additional trajectories are necessary to better characterize the "Coil/Other" definition.
Please cite: MC Baxa, EJ Haddadian, JM Jumper, KF Freed, TR Sosnick. Loss of conformational entropy protein folding calculated using realistic ensembles and its implications for NMR-based calculations. PNAS 2014
W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995
CMBI version by Elmar.Krieger@cmbi.kun.nl / November 18,2002
Questions/Comments: please contact Michael Baxa - firstname.lastname@example.org