The Jameson-Wolf track predicts potential antigenic determinants by combining existing methods for protein structural predictions, using the approach of Jameson and Wolf , 1988. Method results appear as multiple peaks in the Antigenic Index plot, with each peak signifying a potential antigenic determinant. The Antigenic Region graph summarizes the antigenic regions using a threshold value of 1.0. The Jameson-Wolf output is affected by parameter changes made to the Hopp-Woods, Chou-Fasman and Garnier-Robson methods, but not to changes made to the Surface Probability or Karplus-Schulz methods.
In the Tracks panel, expand Immunogenicity, then Antigenicity, and check the box next to Jameson-Wolf. The track will now be visible in the Analysis view
Select the track in the Tracks panel. Open the Track Options section, which appears as follows:
- Broaden Peaks - causes the following smoothing procedure to be applied: For values A[i] that exceed 1.0, where i is a sequence position, find the position p of the peak value within the following 9 residues. If neither structure prediction method predicts helix at position p, apply A[p+n] = A[p+n] + 0.2 * (5 - abs(n)) * A[p] for n = -4 to 4.
- Don’t Broaden Peaks - causes the method to produce the default index of antigenicity by combining values for hydrophilicity (Hopp-Woods, H[<2 > 0.5 <1 > 0 <-1 > -0.5 <-2 > ]), surface probability (Emini, S[<1 > 1.0 <0 > ]), flexibility (Karplus-Schulz, F[<1 > 1.0 <0 > ]), and the secondary structure predictions of Chou-Fasman (CF[ T=2, t=1, 0]) and Garnier-Robson (GR[T=2, t=1, 0]) using the following formula: A = 0.3H + 0.15S + 0.15F +0.2CF + 0.2GR.
Click if you wish to return to the default value.
Need more help with this?