
PFRMAT SS
TARGET T0122
AUTHOR 1956-6867-1656
METHOD New Joint Method and New SSthread 
METHOD We have developed a method for the prediction of protein
METHOD secondary structure using the threading (SSThread),
METHOD which have proposed by Ito et al., by including 
METHOD the score of local sequence homology.
METHOD The structural library for the threading contains 1692 protein
METHOD chains, which were selected from PDB at July 11, 2000
METHOD by using the system for PDB-REPRDB: a database of representative
METHOD protein chains from the PDB at the PAPIA WWW server
METHOD (http://www.rwcp.or.jp/papia/).
METHOD All selected protein chains are of < 30 identity with one another.
METHOD We predict the secondary structure of protein by the New Joint Method
METHOD and New SSThread. The New Joint method takes priority of the prediction,
METHOD when the structure with high score is not found by the threading.
METHOD K. Nishikawa and T. Noguchi: 
METHOD Methods in Enzymology, Vol.202, pp.31-44 (1991). 
METHOD M. Ito, Y. Matsuo and K. Nishikawa: 
METHOD Comput. Appl. Biosci. Vol.13, pp.415-423 (1997).
MODEL  1
M C 0.8
F C 0.8
K C 1.0
D C 1.0
G C 1.0
S C 1.0
L E 0.6
I E 0.8
P E 0.8
Y E 0.6
L E 0.8
T E 0.6
A C 1.0
G C 1.0
D C 1.0
P C 1.0
D C 1.0
K C 1.0
Q C 0.8
S C 0.6
T H 0.6
L H 0.6
N H 0.6
F H 0.6
L H 0.6
L H 0.6
A H 0.6
L H 0.8
D H 0.8
E H 0.6
Y H 0.6
A C 0.6
G C 1.0
A C 0.2
I E 0.6
E E 1.0
L E 0.8
G E 0.6
I C 0.6
P C 0.8
F C 0.8
S C 1.0
D C 1.0
P C 1.0
I C 1.0
A C 1.0
D C 1.0
G C 1.0
K C 1.0
T C 0.8
I C 0.8
Q H 0.6
E H 0.6
S H 0.6
H H 0.8
Y H 1.0
R H 1.0
A H 1.0
L H 1.0
K H 0.8
N H 0.2
G C 0.8
F C 0.8
K H 0.2
L H 0.6
R H 0.6
E H 0.6
A H 0.8
F H 0.8
W H 0.8
I H 0.8
V H 0.8
K H 1.0
E H 1.0
F H 0.8
R H 0.8
R C 0.8
H C 0.8
S C 1.0
S C 1.0
T C 1.0
P C 0.8
I E 1.0
V E 1.0
L E 1.0
M E 1.0
T E 1.0
Y E 0.6
Y C 0.8
N C 1.0
P C 0.8
I C 0.8
Y C 0.2
R H 0.2
A H 0.2
G H 0.2
V H 0.8
R H 1.0
N H 0.8
F H 1.0
L H 1.0
A H 1.0
E H 1.0
A H 1.0
K H 0.6
A H 0.6
S C 0.6
G C 0.8
V C 1.0
D C 1.0
G C 0.6
I E 1.0
L E 1.0
V E 1.0
V E 1.0
D C 0.2
L C 0.6
P C 0.8
V C 0.6
F C 0.6
H C 0.6
A H 0.6
K H 0.6
E H 0.6
F H 0.6
T H 0.8
E H 0.8
I H 0.8
A H 0.8
R H 0.8
E H 1.0
E C 0.2
G C 0.6
I C 0.6
K E 0.2
T E 0.8
V E 1.0
F E 1.0
L E 1.0
A C 0.6
A C 1.0
P C 1.0
N C 1.0
T C 1.0
P C 1.0
D C 0.8
E C 0.8
R C 0.6
L C 0.2
K E 0.6
V E 0.6
I E 0.6
D C 0.8
D C 0.8
M H 0.6
T H 0.2
T H 0.6
G H 0.2
F C 0.2
V E 0.8
Y E 0.8
L E 0.8
V E 0.8
S E 0.8
L E 0.8
Y C 0.6
G C 1.0
T C 1.0
T C 1.0
G C 1.0
A C 1.0
R C 0.8
E C 0.6
E C 0.6
I C 0.6
P C 0.6
K H 0.6
T H 0.8
A H 1.0
Y H 1.0
D H 1.0
L H 1.0
L H 1.0
R H 1.0
R H 1.0
A H 1.0
K H 0.8
R H 0.8
I H 0.8
C C 0.6
R C 0.8
N C 1.0
K C 1.0
V E 0.6
A E 0.8
V E 0.8
G E 0.6
F E 0.8
G E 0.6
V C 0.6
S C 0.8
K C 1.0
R C 0.6
E H 0.8
H H 0.6
V H 0.8
V H 0.6
S H 0.6
L H 0.6
L H 0.8
K H 0.6
E C 0.8
G C 0.8
A C 1.0
N C 1.0
G C 0.6
V E 1.0
V E 1.0
V E 0.8
G C 0.6
S C 0.8
A H 0.8
L H 0.6
V H 0.6
K H 0.6
I H 0.2
I H 0.6
G H 0.6
E C 0.8
K C 0.8
G C 0.8
R C 0.6
E H 0.6
A H 1.0
T H 1.0
E H 1.0
F H 1.0
L H 1.0
K H 1.0
K H 1.0
K H 1.0
V H 1.0
E H 1.0
E H 1.0
L H 1.0
L H 1.0
G H 0.8
I H 0.6
END


