
PFRMAT SS
TARGET T0086
AUTHOR 4608-9149-9325
REMARK
METHOD  HMMSTR: A hidden Markov model based on the I-sites
METHOD  Library of sequence-structure motifs.
METHOD  Chris Bystroff, Vesteinn Thorsson & David Baker
METHOD  =========================================================
METHOD Steps used to generate SS predictions
METHOD (1) Psi-blast was used to obtain an alignment.
METHOD     A sequence profile was summed from the alignment.
METHOD (2) HMMSTR (Bystroff, Thorsson, Baker JMB, in press July 2000) 
METHOD     was used to predict Markov states for each residue. 
METHOD     HMMSTR is a hidden Markov model based on the I-sites Library 
METHOD     of sequence-structure motifs. (Bystroff & Baker, 
METHOD     JMB 281:565-577(1998)) HMMSTR Markov states represent 
METHOD     positions within local structure motifs.
METHOD     HMMSTR secondary structure predictions were done using
METHOD     a model optimized for the prediction of 3 states (HMMSTR-D).
METHOD     Details in the forthcoming JMB paper.
METHOD     Look for an automated HMMSTR server to appear at
METHOD     isites.bio.rpi.edu/hmmstr/hmmstr.html
METHOD     
MODEL 1
S C 0.50
H C 0.50
P C 0.50
A C 0.40
L H 0.40
T H 0.40
Q H 0.60
L H 0.70
R H 0.60
A H 0.70
L H 0.70
R H 0.70
Y H 0.50
C H 0.40
K H 0.40
E C 0.50
I C 0.60
P C 0.70
A C 0.60
L C 0.60
D C 0.70
P C 0.50
Q C 0.50
L C 0.40
L H 0.50
D H 0.50
W H 0.50
L H 0.50
L H 0.40
L H 0.30
E H 0.30
D H 0.40
S H 0.40
M H 0.50
T H 0.50
K H 0.60
R H 0.60
F H 0.60
E H 0.60
Q H 0.50
Q C 0.50
G C 0.80
K C 0.70
T E 0.50
V E 0.60
S E 0.60
V E 0.60
T E 0.50
M E 0.40
I C 0.30
R C 0.40
E C 0.60
G C 0.70
F C 0.50
V C 0.50
E C 0.50
Q C 0.60
N C 0.70
E C 0.60
I C 0.60
P C 0.60
E C 0.60
E C 0.50
L C 0.60
P C 0.60
L C 0.50
L C 0.60
P C 0.60
K H 0.40
E H 0.40
S H 0.50
R H 0.60
Y H 0.60
W H 0.60
L H 0.60
R H 0.60
E H 0.60
I H 0.50
L E 0.40
L E 0.40
C C 0.50
A C 0.80
D C 0.80
G C 0.90
E C 0.60
P E 0.50
W E 0.60
L E 0.50
A E 0.40
G C 0.80
R C 0.60
T C 0.40
V E 0.50
V E 0.50
P E 0.40
V C 0.40
S C 0.50
T C 0.50
L C 0.60
S C 0.70
G C 0.70
P H 0.50
E H 0.70
L H 0.70
A H 0.70
L H 0.70
Q H 0.70
K H 0.60
L H 0.50
G C 0.60
K C 0.50
T C 0.70
P C 0.70
L C 0.70
G C 0.60
R E 0.40
Y E 0.60
L E 0.70
F E 0.70
T E 0.50
S C 0.40
S C 0.40
T C 0.40
L C 0.50
T C 0.50
R H 0.50
D H 0.60
F H 0.60
I H 0.60
E H 0.50
I H 0.40
G C 0.70
R C 0.60
D C 0.60
A C 0.60
G C 0.60
L C 0.60
W C 0.60
G C 0.70
R C 0.60
R C 0.50
S C 0.40
R C 0.30
L E 0.40
R E 0.40
L E 0.40
S C 0.40
G C 0.70
K C 0.60
P C 0.40
L E 0.30
L E 0.30
L E 0.20
T H 0.30
E H 0.30
L H 0.30
F C 0.40
L C 0.60
P C 0.70
A C 0.60
S C 0.70
P C 0.60
L C 0.60
Y C 0.40
END

