
PFRMAT SS
TARGET T0101
AUTHOR 4970-8961-6479
REMARK
METHOD  HMMSTR: A hidden Markov model based on the I-sites
METHOD  Library of sequence-structure motifs.
METHOD  Chris Bystroff, Yu Shao, Vesteinn Thorsson, David Baker 
METHOD  =========================================================
METHOD Steps used to generate TS predictions
METHOD (1) Psi-blast was used to obtain an 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 (3) A set of nearest-neighbor fragments was found for each       
METHOD     3 and 9-residue fragment of the target by       
METHOD     comparing the Markov states in the target fragment
METHOD     to the Markov states in all fragments of all proteins of   
METHOD     known structure.          
METHOD (4) The fragments are the moveset for Monte Carlo Fragment       
METHOD     Insertion as performed by Rosetta 
METHOD     (Simons et al, PNAS 1998) 
METHOD (5) 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 
A C 0.60
D C 0.70
C C 0.70
S C 0.70
S C 0.70
D C 0.60
L C 0.60
T C 0.60
S C 0.70
G C 0.70
I C 0.70
S C 0.70
T C 0.70
K C 0.60
R C 0.50
I E 0.60
Y E 0.70
Y E 0.70
V E 0.70
A E 0.40
P C 0.70
N C 0.80
G C 0.80
N C 0.80
S C 0.60
S C 0.60
N C 0.80
N C 0.80
G C 0.80
S C 0.70
S C 0.50
F C 0.40
N C 0.60
A C 0.60
P C 0.50
M C 0.40
S C 0.30
F H 0.40
S H 0.40
A H 0.40
A H 0.40
M H 0.40
A H 0.30
A C 0.30
V C 0.50
N C 0.70
P C 0.80
G C 0.80
E C 0.60
L E 0.60
I E 0.70
L E 0.70
L E 0.60
K E 0.40
P C 0.60
G C 0.80
T C 0.60
Y C 0.40
T E 0.50
I E 0.50
P E 0.40
Y C 0.40
T C 0.50
Q C 0.60
G C 0.70
K C 0.80
G C 0.80
N C 0.70
T E 0.60
I E 0.70
T E 0.70
F E 0.60
N E 0.40
K C 0.60
S C 0.70
G C 0.70
K C 0.70
D C 0.70
G C 0.70
A C 0.60
P C 0.40
I E 0.50
Y E 0.70
V E 0.70
A E 0.70
A E 0.50
A E 0.40
N C 0.60
C C 0.70
G C 0.70
R C 0.50
A E 0.50
V E 0.50
F E 0.50
D E 0.40
F C 0.50
S C 0.60
F C 0.70
P C 0.70
D C 0.70
S C 0.60
Q C 0.50
W C 0.40
V C 0.40
Q C 0.40
A C 0.40
S C 0.40
Y C 0.50
G C 0.50
F C 0.40
Y C 0.40
V C 0.50
T C 0.60
G C 0.70
D C 0.70
Y C 0.50
W C 0.50
Y C 0.50
F C 0.50
K C 0.60
G C 0.60
V E 0.40
E E 0.50
V E 0.50
T E 0.40
R C 0.40
A C 0.50
G C 0.60
Y C 0.60
Q C 0.60
G C 0.40
A E 0.60
Y E 0.70
V E 0.60
I C 0.40
G C 0.70
S C 0.70
H C 0.70
N C 0.70
T C 0.50
F C 0.40
E C 0.40
N C 0.40
T C 0.30
A E 0.30
F C 0.30
H C 0.40
H C 0.50
N C 0.60
R C 0.70
N C 0.80
T C 0.70
G C 0.40
L E 0.50
E E 0.60
I E 0.50
N C 0.50
N C 0.60
G C 0.80
G C 0.80
S C 0.80
Y C 0.70
N C 0.60
T C 0.40
V E 0.50
I E 0.50
N C 0.50
S C 0.60
D C 0.60
A C 0.60
Y C 0.60
R C 0.70
N C 0.80
Y C 0.80
D C 0.80
P C 0.80
K C 0.80
K C 0.80
N C 0.80
G C 0.80
S C 0.80
M C 0.80
A C 0.80
D C 0.80
G C 0.70
F C 0.60
G C 0.60
P C 0.60
K C 0.50
Q C 0.50
K C 0.60
Q C 0.70
G C 0.80
P C 0.80
G C 0.80
N C 0.70
R C 0.50
F C 0.50
V C 0.50
G C 0.50
C C 0.40
R E 0.40
A C 0.40
W C 0.50
E C 0.60
N C 0.70
S C 0.80
D C 0.80
D C 0.80
G C 0.80
F C 0.70
D C 0.70
L C 0.60
F C 0.70
D C 0.80
S C 0.80
P C 0.80
Q C 0.80
K C 0.50
V E 0.60
V E 0.70
I E 0.70
E E 0.50
N C 0.60
S C 0.60
W C 0.50
A C 0.50
F C 0.50
R C 0.60
N C 0.80
G C 0.90
I C 0.90
N C 0.80
Y C 0.80
W C 0.90
N C 0.90
D C 0.90
S C 0.90
A C 0.90
F C 0.90
A C 0.90
G C 0.90
N C 0.90
G C 0.90
N C 0.90
G C 0.80
F C 0.80
K C 0.80
L C 0.80
G C 0.90
G C 0.90
N C 0.90
Q C 0.90
A C 0.80
V C 0.80
G C 0.80
N C 0.80
H C 0.80
R C 0.70
I C 0.70
T C 0.70
R C 0.80
S C 0.80
V C 0.80
A C 0.80
F C 0.80
G C 0.80
N C 0.90
V C 0.80
S C 0.80
K C 0.80
G C 0.90
F C 0.90
D C 0.90
Q C 0.90
N C 0.90
N C 0.90
N C 0.90
A C 0.90
G C 0.80
G C 0.70
V C 0.60
T C 0.60
V C 0.60
I C 0.60
N C 0.70
N C 0.80
T C 0.70
S C 0.60
Y C 0.70
K C 0.70
N C 0.80
G C 0.80
I C 0.70
N C 0.60
Y C 0.60
G C 0.70
F C 0.70
G C 0.70
S C 0.80
N C 0.70
V C 0.70
Q C 0.80
S C 0.80
G C 0.80
Q C 0.80
K C 0.70
H C 0.50
Y C 0.40
F C 0.40
R C 0.50
N C 0.60
N C 0.70
V C 0.50
S C 0.40
L E 0.40
S C 0.40
A C 0.40
S C 0.40
V E 0.40
T C 0.40
V C 0.50
S C 0.60
N C 0.60
A C 0.60
D C 0.70
A C 0.70
K C 0.70
S C 0.70
N C 0.70
S C 0.70
W C 0.70
D C 0.80
T C 0.80
G C 0.80
P C 0.80
A C 0.70
A C 0.70
S C 0.70
A C 0.70
S C 0.70
D C 0.70
F C 0.50
V C 0.40
S C 0.50
L C 0.50
D C 0.50
T C 0.40
S E 0.40
L E 0.50
A E 0.50
T E 0.50
V E 0.50
S C 0.40
R C 0.60
D C 0.70
N C 0.80
D C 0.80
G C 0.80
T C 0.70
L C 0.50
P C 0.60
E C 0.50
T C 0.60
S C 0.50
L C 0.40
F E 0.40
R C 0.40
L C 0.40
S C 0.60
A C 0.60
N C 0.60
S C 0.50
K C 0.30
L E 0.30
I C 0.30
N C 0.50
A C 0.70
G C 0.80
T C 0.70
K C 0.70
E C 0.60
S C 0.60
N C 0.50
I C 0.40
S C 0.50
Y C 0.50
S C 0.60
G C 0.80
S C 0.80
A C 0.70
P C 0.60
D C 0.60
L C 0.40
G C 0.40
A C 0.40
F H 0.40
E H 0.40
R C 0.40
N C 0.50
END

