dd_randcoil

Random-coil model for an unfolded peptide/protein

Syntax

info = dd_randcoil()
P = dd_randcoil(r,param)
Parameters
  • r - Distance axis (N-array)
  • param - Model parameters
Returns
  • P - Distance distribution (N-array)
  • info - Model information (struct)

Model

../_images/model_scheme_dd_randcoil.png

P(r) = \frac{3}{(2\pi\nu_0)^{3/2}}4\pi r^2\exp(-\frac{3 r^2}{\nu_0})

where \nu_0 = 3/(12\pi r_0 N \nu)^{3/2}

Variable Symbol Default Lower Upper Description
param(1) N 50 2 1000 Number of residues
param(2) R_0 0.20 0.10 0.40 Segment length
param(3) \nu 0.60 0.33 1.00 Scaling exponent

Example using default parameters:

../_images/model_dd_randcoil.png

Description

info = dd_randcoil()

Returns an info structure containing the specifics of the model:

  • info.model - Full name of the parametric model.
  • info.nparam - Total number of adjustable parameters.
  • info.parameters - Structure array with information on individual parameters.
P = dd_randcoil(r,param)

Computes the model distance distribution P of residue-to-residue distances r according to the parameters array param. The required parameters can also be found in the info structure.

References

[1] N. C. Fitzkee, G. D. Rose, PNAS 2004, 101(34), 12497-12502 DOI: 10.1073/pnas.0404236101