
PFRMAT SS
TARGET T0088
AUTHOR 9521-1365-5893
METHOD Program Name: PSIPRED
METHOD Synopsis: Neural network prediction based on PSIBLAST output
METHOD Five neural networks are used to predict secondary structure directly
METHOD from the profiles generated by PSIBLAST. Networks 1-4 predict
METHOD secondary structure, the 5th network filters the output of the first
METHOD level networks. The first level networks have 17*21 inputs and 75 hidden
METHOD units, the second level network has 17*3 inputs and 55 hidden units.
METHOD The networks have been trained on a set of 2937 proteins with
METHOD early-stopped training. 10% of the training data was used to detect
METHOD convergence.
METHOD The target sequence was scanned against a non-redundant databank of
METHOD filtered protein sequences (> 500,000 sequences), with 3 PSIBLAST
METHOD iterations.
MODEL  1
A C 0.48
V E 0.04
S E 0.08
F E 0.07
I E 0.05
G C 0.10
S C 0.21
T C 0.23
E C 0.24
N C 0.24
D C 0.27
V C 0.33
G C 0.35
P C 0.38
S C 0.38
Q C 0.39
G C 0.36
S C 0.29
Y C 0.24
S C 0.19
S C 0.17
T C 0.16
H C 0.16
A C 0.20
M C 0.25
D C 0.30
N C 0.35
L C 0.34
P C 0.32
F E 0.25
V E 0.25
Y E 0.33
N E 0.41
T C 0.33
G C 0.30
Y C 0.26
N C 0.32
I C 0.29
G C 0.27
Y C 0.23
Q C 0.23
N C 0.25
A C 0.22
N C 0.19
V E 0.22
W E 0.30
R E 0.29
I E 0.28
S C 0.16
G C 0.14
G C 0.12
F E 0.15
C E 0.24
V E 0.27
G E 0.29
L C 0.25
D C 0.33
G C 0.24
K C 0.15
V C 0.26
D C 0.38
L C 0.50
P E 0.10
V E 0.12
V E 0.08
G E 0.03
S C 0.09
L C 0.24
D C 0.30
G C 0.21
Q C 0.12
S E 0.03
I E 0.05
Y E 0.07
G C 0.30
L C 0.25
T C 0.19
E H 0.11
E H 0.15
V C 0.38
G C 0.39
L E 0.35
L E 0.41
I E 0.43
W E 0.34
M E 0.26
G C 0.15
D C 0.27
T C 0.32
N C 0.28
Y C 0.29
S C 0.31
R C 0.26
G C 0.23
T C 0.31
A C 0.24
M C 0.30
S C 0.35
G C 0.33
N C 0.24
S C 0.16
W H 0.31
E H 0.29
N H 0.24
V H 0.13
F H 0.07
S H 0.01
G C 0.09
W E 0.01
C E 0.01
V C 0.19
G C 0.19
N C 0.19
Y C 0.19
V C 0.20
S C 0.17
T C 0.19
Q C 0.17
G C 0.15
L E 0.39
S E 0.41
V E 0.42
H E 0.30
V E 0.28
R E 0.35
P E 0.40
V E 0.43
I E 0.44
L E 0.35
K E 0.27
R C 0.13
N C 0.28
S C 0.30
S C 0.25
A C 0.21
Q E 0.05
Y E 0.15
S E 0.21
V E 0.23
Q E 0.20
K E 0.17
T C 0.01
S C 0.10
I C 0.15
G C 0.20
S E 0.09
I E 0.23
R E 0.24
M E 0.25
R C 0.18
P C 0.23
Y C 0.32
N C 0.39
G C 0.42
S C 0.45
S C 0.49
END

