
PFRMAT SS
TARGET T0100
AUTHOR 4970-8961-6479
REMARK
METHOD  HMMSTR: A hidden Markov model based on the I-sites
METHOD  Library of sequence-structure motifs.
METHOD  Plus the BayesAligner. 
METHOD  Chris Bystroff, Bobby Jo Webb, Yu Shao, 
METHOD  Kirsten Piotrowski & Chip Lawrence
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, JMB 281:565-577(1998))
METHOD     HMMSTR Markov states represent positions within local structure motifs.
METHOD (3) A matrix of Markov state probabilities (gamma matrix) for the
METHOD     target was aligned to a set of all HMMSTR gamma matrices for the proteins
METHOD     in the SCOP database if the template protein sequence was within a factor
METHOD     of two of the target sequence length. The alignment was done using the
METHOD     BayesAligner, which produces a 2D histogram of pairwise match
METHOD     probabilities summed over all possible alignments. 
METHOD     (see Zhu, Liu & Lawrence, Bioinformatics 14(1),25-39(1998))
METHOD (4) An optimal alignment was extracted from the 2D histogram and the
METHOD     this was our AL-format submission.
METHOD     
METHOD Steps used to generate SS predictions
METHOD (3) 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 0.40
T C 0.50
T C 0.60
Y C 0.60
N C 0.50
A E 0.50
V E 0.70
V E 0.70
S E 0.60
K E 0.40
S C 0.60
S C 0.80
S C 0.80
D C 0.80
G C 0.70
K C 0.60
T C 0.50
F H 0.40
K H 0.50
T H 0.50
I H 0.60
A H 0.60
D H 0.60
A H 0.60
I H 0.60
A H 0.50
S H 0.50
A C 0.40
P C 0.60
A C 0.70
G C 0.70
S C 0.70
T C 0.70
P E 0.40
F E 0.70
V E 0.80
I E 0.80
L E 0.80
I E 0.70
K E 0.50
N C 0.50
G C 0.60
V C 0.40
Y E 0.40
N C 0.40
E C 0.40
R E 0.40
L E 0.50
T E 0.60
I E 0.50
T C 0.60
R C 0.70
N C 0.60
N C 0.40
L E 0.70
H E 0.80
L E 0.70
K E 0.60
G C 0.50
E C 0.70
S C 0.80
R C 0.70
N C 0.50
G E 0.50
A E 0.70
V E 0.70
I E 0.70
A E 0.50
A C 0.60
A C 0.70
T C 0.60
A C 0.50
A E 0.40
G E 0.50
T E 0.50
L E 0.50
K C 0.40
S C 0.50
D C 0.70
G C 0.80
S C 0.80
K C 0.70
W C 0.60
G C 0.50
T C 0.50
A C 0.50
G C 0.50
S C 0.40
S C 0.40
T E 0.40
I E 0.50
T E 0.50
I E 0.40
S C 0.40
A C 0.60
K C 0.70
D C 0.60
F C 0.40
S E 0.40
A E 0.40
Q E 0.40
S E 0.50
L E 0.50
T E 0.50
I E 0.50
R E 0.40
N C 0.50
D C 0.80
F C 0.80
D C 0.80
F C 0.80
P C 0.80
A C 0.80
N C 0.80
Q C 0.70
A C 0.60
K C 0.60
S C 0.70
D C 0.70
S C 0.80
D C 0.80
S C 0.80
S C 0.80
K C 0.80
I C 0.80
K C 0.80
D C 0.80
T C 0.70
Q C 0.50
A E 0.50
V E 0.60
A E 0.70
L E 0.70
Y E 0.70
V E 0.70
T E 0.50
K C 0.40
S C 0.70
G C 0.80
D C 0.70
R C 0.50
A E 0.50
Y E 0.70
F E 0.70
K E 0.50
D E 0.40
V C 0.50
S C 0.60
L C 0.50
V C 0.60
G C 0.60
Y C 0.60
Q C 0.60
D C 0.50
T E 0.30
L E 0.40
Y E 0.40
V E 0.40
S C 0.50
G C 0.60
G C 0.60
R C 0.50
S E 0.30
F E 0.40
F E 0.40
S E 0.30
D C 0.40
C C 0.40
R E 0.40
I E 0.40
S C 0.40
G C 0.50
T E 0.40
V E 0.50
D E 0.60
F E 0.60
I E 0.70
F E 0.50
G C 0.60
D C 0.70
G C 0.50
T C 0.30
A E 0.50
L E 0.50
F E 0.40
N C 0.30
N C 0.50
C C 0.40
D E 0.30
L E 0.40
V E 0.40
S C 0.40
R C 0.50
Y C 0.60
R C 0.80
A C 0.80
D C 0.80
V C 0.80
K C 0.70
S C 0.70
G C 0.70
N C 0.60
V C 0.40
S C 0.40
G E 0.40
Y E 0.40
L C 0.40
T C 0.50
A C 0.60
P C 0.70
S C 0.70
T C 0.70
N C 0.80
I C 0.80
N C 0.80
Q C 0.80
K C 0.70
Y C 0.60
G C 0.50
L E 0.40
V E 0.50
I E 0.50
T E 0.40
N C 0.50
S C 0.50
R C 0.40
V C 0.40
I C 0.50
R C 0.60
E C 0.70
S C 0.80
D C 0.70
S C 0.60
V C 0.60
P C 0.60
A C 0.60
K C 0.50
S C 0.50
Y C 0.40
G C 0.40
L C 0.50
G C 0.70
R C 0.80
P C 0.80
W C 0.70
H C 0.70
P C 0.60
T C 0.50
T C 0.50
T C 0.50
F C 0.50
S C 0.60
D C 0.70
G C 0.60
R C 0.50
Y C 0.50
A C 0.60
D C 0.70
P C 0.70
N C 0.70
A C 0.60
I C 0.60
G C 0.60
Q C 0.40
T E 0.60
V E 0.70
F E 0.60
L E 0.50
N E 0.40
T C 0.50
S C 0.50
M C 0.50
D C 0.50
N C 0.50
H C 0.40
I C 0.40
Y C 0.50
G C 0.60
W C 0.60
D C 0.60
K C 0.60
M C 0.60
S C 0.70
G C 0.80
K C 0.80
D C 0.70
K C 0.70
N C 0.60
G C 0.60
N C 0.60
T C 0.50
I C 0.40
W E 0.40
F C 0.40
N C 0.60
P C 0.60
E C 0.60
D C 0.50
S E 0.40
R E 0.40
F E 0.40
F E 0.40
E E 0.30
Y C 0.40
K C 0.50
S C 0.60
Y C 0.70
G C 0.80
A C 0.80
G C 0.80
A C 0.80
A C 0.70
V C 0.60
S C 0.60
K C 0.50
D C 0.40
R C 0.30
R E 0.30
Q E 0.30
L C 0.30
T C 0.40
D C 0.40
A C 0.50
Q C 0.50
A C 0.50
A C 0.50
E C 0.40
Y C 0.40
T C 0.40
Q C 0.40
S C 0.40
K C 0.30
V C 0.30
L C 0.30
G C 0.30
D C 0.40
W C 0.40
T C 0.50
P C 0.60
T C 0.70
L C 0.70
P C 0.70
END

