
PFRMAT SS
TARGET T0090
AUTHOR 4608-9149-9325
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, 
METHOD JMB 281:565-577(1998)) HMMSTR Markov states represent 
METHOD 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 
METHOD     matrices for the proteins in the SCOP database if
METHOD     the template protein sequence was within a factor of two of
METHOD     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 
METHOD     and the this was our AL-format submission.
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
M C 0.60
L C 0.60
K C 0.60
P C 0.70
D C 0.70
N C 0.70
L C 0.70
P C 0.60
V C 0.50
T C 0.50
F C 0.50
G C 0.60
K C 0.40
N C 0.40
D H 0.40
V H 0.40
E H 0.40
I H 0.40
I H 0.40
A H 0.40
R H 0.40
E H 0.40
T C 0.30
L C 0.40
Y C 0.40
R C 0.50
G C 0.60
F C 0.40
F E 0.40
S E 0.40
L E 0.40
D E 0.30
L C 0.30
Y C 0.40
R C 0.40
F C 0.40
R C 0.40
H C 0.40
R C 0.40
L C 0.50
F C 0.60
N C 0.70
G C 0.70
Q C 0.60
M C 0.50
S C 0.40
H C 0.40
E C 0.30
V C 0.40
R C 0.40
R H 0.40
E H 0.40
I H 0.30
F H 0.30
E C 0.30
R C 0.50
G C 0.60
H C 0.60
A C 0.50
A E 0.40
V E 0.60
L E 0.60
L E 0.60
P E 0.60
F E 0.50
D C 0.50
P C 0.70
V C 0.70
R C 0.80
D C 0.70
E C 0.50
V E 0.50
V E 0.60
L E 0.40
I E 0.40
E C 0.30
Q C 0.40
I C 0.50
R C 0.50
I C 0.50
A C 0.50
A C 0.50
Y C 0.50
D C 0.50
T C 0.60
S C 0.60
E C 0.60
T C 0.60
P C 0.50
W C 0.30
L E 0.40
L E 0.40
E E 0.30
M C 0.40
V C 0.50
A C 0.60
G C 0.70
M C 0.50
I C 0.40
E C 0.50
E C 0.60
G C 0.70
E C 0.60
S C 0.60
V C 0.50
E C 0.40
D H 0.70
V H 0.70
A H 0.70
R H 0.80
R H 0.80
E H 0.80
A H 0.80
I H 0.80
E H 0.70
E H 0.60
A H 0.40
G C 0.70
L C 0.60
I C 0.60
V H 0.30
K H 0.40
R H 0.40
T H 0.40
K H 0.40
P H 0.40
V H 0.40
L H 0.30
S C 0.30
F C 0.30
L C 0.50
A C 0.60
S C 0.70
P C 0.70
G C 0.70
G C 0.70
T C 0.60
S C 0.40
E C 0.40
R H 0.40
S H 0.40
S H 0.40
I H 0.40
M H 0.40
V H 0.40
G H 0.40
E H 0.40
V H 0.40
D H 0.40
A H 0.40
T H 0.40
T C 0.30
A C 0.40
S C 0.40
G C 0.50
I C 0.50
H C 0.50
G C 0.50
L C 0.50
A C 0.50
D C 0.60
E C 0.50
N C 0.50
E C 0.50
D C 0.40
I C 0.30
R C 0.30
V E 0.30
H E 0.30
V E 0.30
V E 0.30
S C 0.40
R H 0.70
E H 0.70
Q H 0.80
A H 0.80
Y H 0.80
Q H 0.80
W H 0.70
V H 0.60
E H 0.50
E C 0.40
G C 0.50
K C 0.50
I C 0.40
D C 0.40
N C 0.40
A H 0.50
A H 0.50
S H 0.60
V H 0.60
I H 0.60
A H 0.70
L H 0.70
Q H 0.70
W H 0.70
L H 0.70
Q H 0.60
L H 0.60
H H 0.50
H H 0.50
Q H 0.60
A H 0.60
L H 0.60
K H 0.60
N H 0.60
E H 0.60
W H 0.60
A H 0.60
END

