PFRMAT SS 
TARGET T0056 
AUTHOR 1751-3146-3362 
METHOD Using neural net fssp-12345-IDaa1-9-6-11-9-3-8-7-ehl-seeded6-trained.net 
METHOD This is a 4-layer network, with  
METHOD	window	units 
METHOD	    9	    6 
METHOD	   11	    9 
METHOD	    3	    8 
METHOD	    7	    3 (1 EHL ) 
METHOD The input amino acid frequencies were determined from 
METHOD alignment t56.t98_6.a2m.gz 
METHOD with weighted counts, using HenikoffWeight(1 bits/column, 0.5) 
METHOD The weighting was determined by the posterior distribution 
METHOD after regularizing with recode3.20comp. 
METHOD Counts were regularized to probabilities using 
METHOD /projects/compbio/lib/recode3.20comp 
METHOD Total sequence weight for alignment was 9.50002 
METHOD 
METHOD Since the submitters provided a secondary structure assignment, 
METHOD predicting it is rather silly, but we include the prediction for 
METHOD completeness.  The prediction is not bad, though there seems to 
METHOD a tendency to predict helix a little past the ends of the 
METHOD reported helices. 
MODEL 1 
M C 0.90 
K C 0.76 
V C 0.85 
P C 0.94 
P C 0.87 
H C 0.69 
S C 0.56 
I H 0.80 
E H 0.94 
A H 0.97 
E H 0.98 
Q H 0.97 
S H 0.96 
V H 0.95 
L H 0.92 
G H 0.87 
G H 0.84 
L H 0.78 
M H 0.58 
L C 0.60 
D C 0.76 
N C 0.55 
E H 0.84 
R H 0.86 
W H 0.96 
D H 0.98 
D H 0.98 
V H 0.98 
A H 0.98 
E H 0.96 
R H 0.90 
V H 0.66 
V C 0.52 
A C 0.53 
D C 0.54 
D H 0.48 
F C 0.53 
Y C 0.50 
T H 0.60 
R H 0.75 
P H 0.80 
H H 0.95 
R H 0.98 
H H 0.99 
I H 0.99 
F H 0.99 
T H 0.99 
E H 0.99 
M H 0.98 
A H 0.98 
R H 0.95 
L H 0.91 
Q H 0.75 
E C 0.61 
S C 0.78 
G C 0.93 
S C 0.95 
P C 0.82 
I C 0.71 
D C 0.61 
L H 0.60 
I H 0.85 
T H 0.80 
L H 0.93 
A H 0.97 
E H 0.97 
S H 0.96 
L H 0.89 
E H 0.64 
R H 0.50 
Q C 0.84 
G C 0.90 
Q C 0.66 
L C 0.52 
D C 0.49 
S C 0.42 
V C 0.53 
G C 0.85 
G C 0.79 
F H 0.58 
A H 0.76 
Y H 0.79 
L H 0.93 
A H 0.96 
E H 0.95 
L H 0.92 
S H 0.86 
K H 0.63 
N C 0.57 
T C 0.66 
P C 0.84 
S C 0.57 
A H 0.73 
A H 0.85 
N H 0.78 
I H 0.96 
S H 0.98 
A H 0.99 
Y H 0.99 
A H 0.99 
D H 0.98 
I H 0.97 
V H 0.97 
R H 0.96 
E H 0.96 
R H 0.97 
A H 0.98 
V H 0.96 
V H 0.97 
R H 0.97 
E H 0.95 
M H 0.92 
I H 0.85 
S H 0.63 
END 
