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
  • Glycine residues
  • Pre-proline residues
  • Proline residues

    Output:
    [residue] [amino acid] [secondary structure] [# of sidechain rotamers] [backbone entropy loss] [sidechain entropy loss] [total entropy loss]

    Assumptions:
  • 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

    *DSSP COPYRIGHT:
      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 - baxa@uchicago.edu