Probabilistic Secondary Structure of the Protein

 

 

ADAPT-NMR provides probabilistic secondary structure of the protein in PECAN format (A jpg file and a text file).

The image and the text of PECAN output is shown as annotated images below.   The following tags are used to identify the structure.

_PECAN.Extended_probability

The probability for the given residue to be in Extended (Beta Sheet) state

_PECAN.Helix_probability

The probability for the given residue to be in Alpha Helical state

_PECAN.Extended_boundary_designator

a value of 1 (one) indicates PECAN designation of the residue as a boundary residue in an Extended region

_PECAN.Helix_boundary_designator

a value of 1 (one) indicates PECAN designation of the residue as a boundary residue in a Helical region

When the probability for a given state is less than one, the remainder indicates the probability of being in "other" state.

Description: Description: Description: http://pine.nmrfam.wisc.edu/PECAN/pecan_fig.jpg

NPDPlot tool in NMRFAM-Sparky package can be used to analyze the result interactively.
Open "npdplot.ini" file in the NPDPlot.


Description: Description: Description: http://pine.nmrfam.wisc.edu/PECAN/PECAN.JPG