Example for requesting to return the 1D structure prediction in CASP2 format

Bold face: keyword "return phd casp2"

What is CASP2?
CASP2 was the second protein structure prediction contest organised by John Moult, and held in Asilomar, California in Dec. 1996. The following format was obligatory to submit predictions to CASP2 (Europe, USA).

Input (request of you)

Joe Sequencer, Department of Advanced Protein Research,
National Univeristy, Timbuktu
joe@amino.churn.edu
return phd casp2   
# sh3 
KELVLALYDYQEKSPREVTMKKGDILTL
LNSTNKDWWKVEVNDRQGFVPAAYVKKLD

Output (result returned)

Block with sequence alignment.
Block with information about prediction method.
Block with prediction in default format.
Block with prediction in CASP2 format (shown here):

Explanations:

1st column sequence in one-letter code
2nd column A secondary structure in three states helix H, strand E, rest L
2nd column B relative residue solvent accessibility
3rd column strength of prediction (0 low, 1 high)

PHD prediction in CASP2 format

PFRMAT ABF1
TARGET t3_27793
AUTHOR your_name and your_email
REMARK Automatic usage of PHDsec and PHDacc
REMARK AUTHOR:   B Rost
REMARK TITLE:    PHD: predicting 1D protein structure by profile based neural networks
REMARK JOURNAL:  Meth. in Enzym, 1996, 266, 525-539
BEGDAT 1.1 1  0.7
SS     56
E  C   0.40
L  E   0.90
V  E   1.00
L  E   1.00
A  E   1.00
L  E   1.00
Y  E   0.90
D  E   0.30
Y  C   0.50
Q  C   0.90
E  C   0.90
K  C   0.80
S  C   0.90
P  C   0.50
R  C   0.30
E  C   0.20
V  E   0.30
T  E   0.50
M  E   0.50
K  C   0.50
K  C   0.90
G  C   1.00
D  C   0.80
I  E   0.90
L  E   1.00
T  E   1.00
L  E   0.90
L  E   0.50
N  C   0.80
S  C   0.90
T  C   1.00
N  C   0.90
K  C   0.40
D  C   0.40
W  C   0.30
W  E   0.60
K  E   0.70
V  E   0.70
E  C   0.30
V  C   0.60
N  C   0.70
D  C   1.00
R  C   0.90
Q  C   0.40
G  E   0.30
F  E   0.20
V  E   0.20
P  C   0.30
A  C   0.30
A  C   0.20
Y  C   0.30
V  E   0.30
K  E   0.20
K  E   0.20
L  C   0.50
D  C   1.00
ACC     56
E   49   0.60
L    0   0.20
V    0   0.80
L    0   0.40
A    0   1.00
L    0   1.00
Y    0   0.40
D   36   0.20
Y    0   0.20
Q   49   0.40
E   49   0.40
K   49   0.60
S   36   0.20
P   49   0.50
R   49   0.60
E   49   0.50
V    0   0.30
T   36   0.20
M    0   0.30
K   49   0.60
K   49   0.60
G    0   0.10
D   49   0.40
I   36   0.20
L    0   0.60
T   36   0.30
L    0   0.70
L    0   0.50
N   49   0.50
S   49   0.60
T   49   0.50
N   49   0.50
K   49   0.60
D   49   0.40
W    0   0.20
W    0   0.40
K   49   0.50
V    0   0.40
E   36   0.30
V   49   0.30
N   49   0.60
D   49   0.50
R   49   0.50
Q   49   0.50
G    0   0.40
F    0   0.10
V    0   0.40
P    0   0.40
A    0   0.20
A   49   0.40
Y    0   0.30
V    0   0.60
K   36   0.20
K   49   0.50
L    0   0.10
D   81   0.80
ENDDAT 1.1
END