PFRMAT SS 
TARGET T0079 
AUTHOR 6323-3724-9414 
METHOD Program Name: PSIPRED 
METHOD Synopsis: Neural network prediction based on PSIBLAST output 
METHOD Two neural networks are used to predict secondary structure directly 
METHOD from the profiles generated by PSIBLAST. The first network predicts 
METHOD secondary structure, the second network filters the output of the first 
METHOD network. The first network has 17*21 inputs and 75 hidden units, the 
METHOD second network has 17*3 inputs and 55 hidden units. The networks have 
METHOD been trained on a set of 1887 proteins with early-stopped training. 
METHOD 10% of the training data was used to detect convergence. 
METHOD 
METHOD The target sequence was scanned against a non-redundant databank of 
METHOD filtered protein sequences (276030 sequences), with 3 PSIBLAST 
METHOD iterations. 
MODEL  1 
M C 0.94 
T C 0.76 
M C 0.45 
S C 0.50 
R C 0.50 
R C 0.49 
N C 0.72 
T C 0.58 
D C 0.58 
A H 0.17 
I H 0.80 
T H 0.88 
I H 0.94 
H H 0.95 
S H 0.95 
I H 0.95 
L H 0.96 
D H 0.95 
W H 0.96 
I H 0.94 
E H 0.88 
D H 0.71 
N C 0.43 
L C 0.60 
E C 0.89 
S C 0.92 
P C 0.90 
L C 0.85 
S C 0.90 
L H 0.77 
E H 0.86 
K H 0.91 
V H 0.94 
S H 0.95 
E H 0.94 
R H 0.85 
S H 0.66 
G C 0.68 
Y C 0.89 
S C 0.93 
K H 0.76 
W H 0.89 
H H 0.93 
L H 0.94 
Q H 0.95 
R H 0.96 
M H 0.95 
F H 0.96 
K H 0.95 
K H 0.85 
E H 0.70 
T C 0.06 
G C 0.89 
H C 0.93 
S C 0.89 
L H 0.79 
G H 0.89 
Q H 0.92 
Y H 0.95 
I H 0.95 
R H 0.96 
S H 0.96 
R H 0.95 
K H 0.95 
M H 0.95 
T H 0.95 
E H 0.95 
I H 0.95 
A H 0.95 
Q H 0.95 
K H 0.94 
L H 0.89 
K H 0.73 
E H 0.06 
S C 0.78 
N C 0.91 
E C 0.88 
P C 0.86 
I H 0.81 
L H 0.86 
Y H 0.90 
L H 0.94 
A H 0.95 
E H 0.93 
R H 0.80 
Y H 0.32 
G C 0.67 
F C 0.91 
E C 0.90 
S C 0.86 
Q H 0.70 
Q H 0.81 
T H 0.91 
L H 0.94 
T H 0.95 
R H 0.96 
T H 0.95 
F H 0.95 
K H 0.93 
N H 0.80 
Y H 0.63 
F H 0.18 
D C 0.86 
V C 0.94 
P C 0.95 
P H 0.78 
H H 0.86 
K H 0.90 
Y H 0.94 
R H 0.95 
M H 0.91 
T H 0.80 
N H 0.37 
M C 0.67 
Q C 0.75 
G C 0.78 
E C 0.70 
S C 0.72 
R C 0.79 
F C 0.63 
L C 0.62 
H C 0.47 
P C 0.59 
L C 0.71 
N C 0.75 
H C 0.83 
Y C 0.81 
N C 0.82 
S C 0.95 
END 
