Dear Linda,
I will reproduce an e-letter that Eric Cabot of GCG sent me
when I asked the same questions. I believe that it
answers everything but the method used in the Hydrophobicity
column, which we are still vague on.
Best wishes,
Rich
Richard,
Here is the correspondance between the terms used in the
Chou &
Fasman papers and PEPPLOT.
==========================================
C&F PEPPLOT
============ ============
Pa Alpha Stat = Pa /100
<Pa> Alpha Ave = <Pa>/100
Pb Beta Stat = Pb/100
<Pb> Beta Ave = Pa/100
<pt> Turn = Pb/10,000
==========================================
For example, here is a comparison of the dataset analyzed
in Prevelige and
Fasman (1989) and PEPPLOT (only the first line is shown
here):
PEPPLOT:
Alpha Alpha Beta Beta Alpha Beta
Pos Res Stat Ave Stat Ave NH2 COOH NH2 COOH Turn HPhob
------------------------------------------------------------
------------ ..
1 A 1.42 1.09 0.83 1.10 0.68 0.68 1.23 0.39 0.39 0.00
Prevelige and Fasman:
Pa <Pa> Pb <Pb> <pt>
142 109 83 109 3.9 x 10^-5
The following are not mentioned in the Chou and Fasman
papers but are
documented in the PEPPLOT chapter of the GCG Program Manual:
Alpha NH2 - not mentioned in C&F paper
Alpha COOH "
Beta NH2 "
Beta COOH "
I hope that this clarifies matters for you somewhat.
Regards,
Eric L. Cabot, Ph.D.
