
PFRMAT SS
TARGET T0101
AUTHOR 4608-9149-9325
REMARK
METHOD  Automated I-SITES / ROSETTA
METHOD  =========================================================
METHOD  I-sites predicts local structure motifs in the query
METHOD  sequence. These are used by Rosetta to generate the 
METHOD  3D structure by fragment insertion Monte Carlo.
METHOD  The output predictions are coordinates. The predictions
METHOD  are ab initio. No fold recognition is done by this server
METHOD  at the current time.
METHOD  The predictions from this server are of local and
METHOD  super-local structure. They should be evaluated
METHOD  on an approximate length scale of 30-60 residues. 
METHOD  Some effort is made by the program to pack the local structure
METHOD  into a globally-globular form.
METHOD  =========================================================
METHOD Steps used to generate TS predictions
METHOD (1) Psi-blast was used to obtain an alignment
METHOD (2) The PHD prediction server was used to obtain a 3-state 
METHOD     prediction (optional)
METHOD (3) The I-sites method (JMB 281(3):565-577)
METHOD     was used to predict backbone angles and 
METHOD     confidences. Backbone angle confidnces are reflected in
METHOD     the B-column of the PDB output. B = 1.00 + (1.00 - confidence)*10
METHOD     except unpredicted residus (B = 0.00)
METHOD (4) Non-conserved non-polar sidechains were converted to their
METHOD     most likely polar counterpart. This would, we hope, restrict
METHOD     core residues to conserved non-polar sidechains.
METHOD (5) Fragment insertion Monte Carlo folding (ROSETTA, Simons et al
METHOD     PNAS 1999) was used to build a 3D structure from the
METHOD     fragment library output by I-sites. Residues with I-sites
METHOD     confidences > 0.75 were restrained to their predicted backbone
METHOD     angles. For longer sequences, the protein was broken up into
METHOD     segments containing 50 un-restrained residues (typically 100
METHOD     residues). 
METHOD (6) The 3D structure with the best score was selected, its
METHOD     sequence replaced with the original one. For long sequences
METHOD     A simple genetic algorithm was employed to find the
METHOD     optimum points of recombination, using the same scoring function
METHOD     as above (ROSETTA).
METHOD 
METHOD >>>>THIS METHOD IS TOTALLY AUTOMATED!! <<<<
METHOD URL http://honduras.bio.rpi.edu/~isites/ISL_rosetta.html
METHOD     
MODEL 1  
A C 0.70
D C 0.70
C C 0.70
S C 0.70
S C 0.70
D C 0.70
L C 0.60
T C 0.60
S C 0.70
G C 0.80
I C 0.70
S C 0.70
T C 0.50
K C 0.50
R E 0.40
I E 0.60
Y E 0.60
Y E 0.60
V E 0.50
A C 0.50
P C 0.70
N C 0.80
G C 0.80
N C 0.70
S C 0.60
S C 0.60
N C 0.70
N C 0.80
G C 0.80
S C 0.70
S C 0.60
F C 0.60
N C 0.60
A C 0.70
P C 0.60
M C 0.50
S C 0.50
F H 0.40
S H 0.60
A H 0.70
A H 0.70
M H 0.70
A H 0.60
A H 0.40
V C 0.50
N C 0.70
P C 0.80
G C 0.80
E C 0.60
L E 0.50
I E 0.70
L E 0.60
L E 0.60
K E 0.40
P C 0.60
G C 0.70
T C 0.50
Y E 0.40
T E 0.50
I C 0.40
P C 0.50
Y C 0.50
T C 0.60
Q C 0.70
G C 0.80
K C 0.70
G C 0.80
N C 0.70
T E 0.40
I E 0.60
T E 0.60
F E 0.50
N E 0.40
K C 0.50
S C 0.70
G C 0.80
K C 0.60
D C 0.70
G C 0.80
A C 0.70
P C 0.40
I E 0.60
Y E 0.70
V E 0.60
A E 0.50
A E 0.40
A C 0.50
N C 0.60
C C 0.70
G C 0.70
R C 0.60
A E 0.40
V E 0.50
F E 0.50
D E 0.40
F C 0.50
S C 0.50
F C 0.70
P C 0.70
D C 0.70
S C 0.40
Q H 0.40
W H 0.40
V H 0.40
Q H 0.40
A H 0.40
S C 0.30
Y C 0.40
G C 0.70
F E 0.50
Y E 0.60
V E 0.60
T E 0.50
G C 0.60
D C 0.70
Y C 0.50
W E 0.40
Y C 0.40
F E 0.40
K C 0.60
G C 0.70
V C 0.60
E E 0.50
V E 0.60
T E 0.50
R C 0.40
A C 0.60
G C 0.70
Y C 0.60
Q C 0.70
G C 0.70
A C 0.50
Y E 0.50
V E 0.60
I E 0.60
G C 0.50
S C 0.60
H C 0.60
N C 0.60
T C 0.60
F C 0.50
E C 0.50
N C 0.50
T C 0.40
A C 0.30
F E 0.30
H C 0.40
H C 0.50
N C 0.60
R C 0.70
N C 0.70
T C 0.70
G C 0.80
L C 0.60
E E 0.40
I E 0.40
N C 0.50
N C 0.70
G C 0.80
G C 0.80
S C 0.60
Y C 0.50
N C 0.50
T C 0.40
V E 0.50
I C 0.40
N C 0.60
S C 0.60
D C 0.50
A C 0.50
Y C 0.50
R C 0.50
N C 0.60
Y C 0.70
D C 0.80
P C 0.80
K C 0.70
K C 0.70
N C 0.80
G C 0.80
S C 0.70
M C 0.50
A C 0.50
D C 0.70
G C 0.70
F C 0.70
G C 0.70
P C 0.60
K C 0.60
Q C 0.60
K C 0.60
Q C 0.60
G C 0.70
P C 0.80
G C 0.80
N C 0.70
R C 0.50
F E 0.40
V C 0.40
G C 0.60
C C 0.50
R C 0.40
A C 0.40
W C 0.40
E C 0.50
N C 0.70
S C 0.70
D C 0.70
D C 0.70
G C 0.70
F C 0.60
D C 0.60
L C 0.40
F C 0.40
D C 0.50
S C 0.70
P C 0.70
Q C 0.70
K E 0.40
V E 0.60
V E 0.70
I E 0.60
E E 0.50
N C 0.60
S C 0.60
W C 0.50
A C 0.40
F C 0.40
R C 0.50
N C 0.70
G C 0.80
I C 0.60
N C 0.50
Y E 0.40
W C 0.40
N C 0.50
D C 0.70
S C 0.60
A C 0.50
F C 0.50
A C 0.60
G C 0.70
N C 0.70
G C 0.70
N C 0.70
G C 0.70
F C 0.50
K C 0.50
L C 0.50
G C 0.60
G C 0.70
N C 0.60
Q C 0.50
A C 0.50
V C 0.50
G C 0.70
N C 0.70
H C 0.50
R C 0.40
I E 0.40
T E 0.40
R C 0.30
S C 0.30
V C 0.30
A C 0.30
F C 0.50
G C 0.60
N C 0.60
V C 0.50
S C 0.60
K C 0.70
G C 0.80
F C 0.70
D C 0.70
Q C 0.70
N C 0.70
N C 0.70
N C 0.70
A C 0.70
G C 0.70
G C 0.60
V E 0.40
T E 0.60
V E 0.70
I E 0.60
N C 0.40
N C 0.70
T C 0.70
S C 0.70
Y C 0.60
K C 0.50
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 0.60
G C 0.70
S C 0.70
N C 0.70
V C 0.60
Q C 0.60
S C 0.70
G C 0.80
Q C 0.70
K C 0.50
H E 0.50
Y E 0.50
F E 0.50
R C 0.40
N C 0.60
N C 0.70
V C 0.50
S E 0.40
L C 0.40
S C 0.40
A C 0.50
S C 0.40
V E 0.50
T E 0.60
V E 0.60
S E 0.40
N C 0.50
A C 0.50
D C 0.60
A C 0.60
K C 0.60
S C 0.60
N C 0.70
S C 0.60
W C 0.50
D C 0.60
T C 0.70
G C 0.70
P C 0.70
A C 0.60
A C 0.60
S C 0.60
A C 0.50
S C 0.50
D C 0.50
F C 0.40
V C 0.30
S C 0.40
L C 0.50
D C 0.60
T C 0.60
S C 0.50
L E 0.40
A E 0.60
T E 0.70
V E 0.70
S E 0.80
R E 0.70
D C 0.60
N C 0.90
D C 0.90
G C 0.80
T C 0.60
L E 0.60
P E 0.50
E C 0.50
T C 0.40
S C 0.40
L E 0.20
F E 0.30
R E 0.30
L E 0.20
S C 0.30
A C 0.40
N C 0.50
S C 0.50
K C 0.40
L E 0.30
I E 0.30
N C 0.40
A C 0.60
G C 0.70
T C 0.70
K C 0.60
E C 0.60
S C 0.60
N C 0.50
I C 0.50
S C 0.50
Y C 0.40
S C 0.50
G C 0.70
S C 0.60
A C 0.70
P C 0.70
D C 0.60
L C 0.50
G C 0.50
A C 0.40
F C 0.30
E C 0.30
R C 0.40
N C 0.40
END

