PFRMAT SS 
TARGET T0057 
AUTHOR 1365-6264-2513 
REMARK Three-state predictions are made with this algorithm, namely, 
REMARK coil(C), helix(H) and beta-sheets(B) 
METHOD The method uses statistical measures calculated on a sample 
METHOD set to make the predictions. The sample data set consists of 
METHOD 306 non-homologous (<25% sequence identity) best resolved 
METHOD (<2 angstrom resolution) PDB structures to calculate three 
METHOD different statistical measures. The three measures used are 
METHOD simple structural propensities, as defined in the Chou-Fasman  
METHOD method. The other two measures are basically conditional  
METHOD propensities of a residue to be in a structural motif, given 
METHOD that a residue or a dipeptide is in its near neighbourhood. 
METHOD We call these to measures dipeptide and tripeptide potentials. 
METHOD Dipeptide potential is defined as follows. We calculate the 
METHOD occurence of a residue in a particular structural motif with 
METHOD another residue at a distance i from it. For example, the 
METHOD occurence of alanine (A) in a helical motif with say a cystine 
METHOD at distance -10 from it. We also calculate the occurence of 
METHOD the residue in non-s under the same conditions. In the example 
METHOD cited it would correspond to the occurence of A in non-helical 
METHOD motif. The ratio of these two numbers is defined as the dipeptide 
METHOD potential. Tripeptide potential is defined in a similar manner 
METHOD in terms of near neighbour dipeptides, except that in this case 
METHOD we do not consider the nature of the central residue, only its 
METHOD structural motif is taken into account. For example, one  
METHOD possible value would be the potential of any residue in a 
METHOD helical structure with the dipeptide AA at distance +5, say. 
METHOD We have considered upto 32 neighbours each in the positive 
METHOD and negative direction from the central residue (amounting to 
METHOD 64 near neighbours). Having generated these three matrices 
METHOD for the three different measures, we go about making our  
METHOD predictions as follows. Having read the sequence we take each 
METHOD residue as central residue and add up the potential values 
METHOD for its nearest neighbours and get a score for all the three  
METHOD measures. For each measure, the score is calculated assuming 
METHOD the central residue to be in each of the three structural 
METHOD motifs considered, namely coil (C), helix (H) and beta-sheets (B). 
METHOD We get three scores for each measure. The structural motif for 
METHOD which the score is the highest is predicted for the central 
METHOD residue. We have considered upto 64 nearest neighbours and 
METHOD find that for simple propensities 6 near neigbours give the 
METHOD best predictions, while for the other two measures best 
METHOD predictions are obtained using all 64 neighbours. Using the 
METHOD predicting potential of individual measures, the overall 
METHOD prediction is made by taking a weighted sum of the individual 
METHOD scores to get the overall score (the prediction potential of 
METHOD each measure defines the weight). Having obtained the weight 
METHOD values by taking the sample set as the test set, we have 
METHOD applied this method to make our predictions for the CASP3 
METHOD targets. 
MODEL  1 
M  E 0.27 
I  E 0.93 
N  E 0.14 
V  E 0.01 
A  E 0.01 
V  E 0.25 
N  E 0.98 
G  E 0.95 
Y  E 0.18 
G  E 0.83 
T  E 0.07 
I  E 0.15 
G  E 0.76 
K  E 0.37 
R  E 0.22 
V  H 0.62 
A  H 0.36 
D  H 0.53 
A  H 0.81 
I  H 0.01 
I  H 0.01 
K  H 0.55 
Q  H 0.01 
P  H 0.01 
D  H 0.71 
M  H 0.93 
K  E 0.81 
L  E 0.01 
V  E 0.17 
G  E 0.01 
V  E 0.01 
A  E 0.48 
K  E 0.87 
T  H 0.46 
S  H 0.20 
P  H 0.67 
N  H 0.38 
Y  H 0.31 
E  H 0.40 
A  H 0.42 
F  E 0.83 
I  E 0.94 
A  E 0.29 
H  E 0.72 
R  E 0.07 
R  E 0.25 
G  E 0.92 
I  E 0.65 
R  E 0.01 
I  E 0.01 
Y  E 0.01 
V  E 0.71 
P  E 0.13 
Q  E 0.05 
Q  E 0.31 
S  E 0.69 
I  E 0.61 
K  E 0.15 
K  E 0.72 
F  E 0.77 
E  C 0.42 
E  C 0.03 
S  C 0.01 
G  C 0.01 
I  C 0.01 
P  C 0.50 
V  C 0.67 
A  E 0.70 
G  E 0.01 
T  E 0.98 
V  H 0.73 
E  H 0.52 
D  H 0.72 
L  H 0.54 
I  E 0.54 
K  E 0.12 
T  E 0.20 
S  E 0.68 
D  E 0.01 
I  E 0.01 
V  E 0.01 
V  E 0.01 
D  E 0.01 
T  C 0.99 
T  C 0.68 
P  C 0.96 
N  C 0.57 
G  C 0.73 
V  H 0.56 
G  H 0.01 
A  H 0.22 
Q  H 0.98 
Y  H 0.27 
K  H 0.05 
P  H 0.96 
I  H 0.01 
Y  H 0.01 
L  H 0.01 
Q  H 0.01 
L  H 0.01 
Q  H 0.01 
R  H 0.16 
N  H 0.01 
A  H 0.31 
I  H 0.94 
F  H 0.23 
Q  H 0.61 
G  C 0.64 
G  C 0.11 
E  C 0.91 
K  C 0.50 
A  C 0.95 
E  C 0.01 
V  H 0.82 
A  H 0.17 
D  H 0.10 
I  H 0.12 
S  H 0.75 
F  H 0.01 
S  H 0.01 
A  H 0.50 
L  H 0.01 
C  H 0.01 
N  H 0.40 
Y  H 0.01 
N  H 0.01 
E  H 0.01 
A  H 0.55 
L  H 0.20 
G  C 0.44 
K  C 0.01 
K  C 0.89 
Y  E 0.95 
I  E 0.01 
R  E 0.01 
V  E 0.01 
V  E 0.57 
S  E 0.57 
C  H 0.98 
N  H 0.23 
T  H 0.51 
T  H 0.01 
A  H 0.15 
L  H 0.98 
L  H 0.27 
R  H 0.56 
T  E 0.01 
I  E 0.01 
C  E 0.01 
T  E 0.01 
V  E 0.49 
N  E 0.50 
K  E 0.01 
V  E 0.80 
S  E 0.01 
K  E 0.61 
V  E 0.46 
E  E 0.25 
K  E 0.01 
V  H 0.43 
R  H 0.50 
A  H 0.44 
T  H 0.50 
I  H 0.55 
V  H 0.29 
R  H 0.28 
R  H 0.74 
A  H 0.32 
A  H 0.30 
D  H 0.01 
Q  H 0.55 
K  H 0.53 
E  E 0.01 
V  E 0.46 
K  E 0.86 
K  E 0.40 
G  E 0.30 
P  E 0.01 
I  E 0.01 
N  E 0.01 
S  E 0.42 
L  E 0.47 
V  C 0.02 
P  C 0.01 
D  C 0.06 
P  C 0.53 
A  C 0.62 
T  C 0.01 
V  C 0.01 
P  C 0.01 
S  C 0.25 
H  C 0.51 
H  C 0.99 
A  C 0.19 
K  C 0.72 
D  C 0.97 
V  H 0.46 
N  H 0.69 
S  H 0.19 
V  H 0.96 
I  H 0.97 
R  H 0.61 
N  H 0.63 
L  H 0.08 
D  H 0.21 
I  H 0.41 
A  H 0.86 
T  H 0.37 
M  C 0.30 
A  C 0.20 
V  C 0.58 
I  C 0.38 
A  C 0.93 
P  H 0.70 
T  H 0.67 
T  H 0.96 
L  H 0.79 
M  H 0.53 
H  H 0.57 
M  H 0.40 
H  H 0.29 
F  H 0.94 
I  H 0.01 
N  H 0.71 
I  H 0.56 
T  H 0.01 
L  H 0.35 
K  H 0.01 
D  H 0.01 
K  H 0.01 
V  H 0.71 
E  H 0.01 
K  H 0.01 
K  H 0.51 
D  H 1.00 
I  H 0.35 
L  H 0.08 
S  H 0.47 
V  H 0.98 
L  H 0.62 
E  C 0.01 
N  C 0.16 
T  C 0.89 
P  E 0.71 
R  E 0.06 
I  E 0.01 
V  E 0.01 
L  E 0.01 
I  E 0.01 
S  E 0.25 
S  H 0.01 
K  H 0.76 
Y  H 0.01 
D  H 0.01 
A  H 0.01 
E  H 0.01 
A  H 0.01 
T  H 0.01 
A  H 0.01 
E  H 0.01 
L  H 0.01 
V  H 0.01 
E  H 0.01 
V  H 0.01 
A  H 0.01 
R  H 0.01 
D  H 0.01 
L  H 0.01 
K  H 1.00 
R  H 0.01 
D  H 0.98 
R  C 0.53 
N  C 0.01 
D  C 0.01 
I  C 0.80 
P  E 0.79 
E  E 0.47 
V  E 0.01 
M  E 0.01 
I  E 0.01 
F  E 0.60 
S  E 0.20 
D  H 0.67 
S  H 0.01 
I  H 0.01 
Y  H 0.01 
V  H 0.01 
K  H 0.47 
D  H 0.01 
D  H 0.05 
E  H 0.01 
V  H 0.01 
M  H 0.01 
L  H 0.56 
M  H 0.01 
Y  H 0.01 
A  H 0.01 
V  H 0.01 
H  H 0.01 
Q  H 0.34 
E  H 0.23 
S  H 0.89 
I  H 0.97 
V  H 0.09 
V  H 0.14 
P  H 0.01 
E  H 0.15 
N  H 0.01 
I  H 0.01 
D  H 0.01 
A  H 0.01 
I  H 0.01 
R  H 0.01 
A  H 0.01 
S  H 0.01 
M  H 0.01 
K  H 0.01 
L  H 0.16 
M  H 0.01 
S  H 0.01 
A  H 0.01 
E  H 0.01 
D  H 0.01 
S  H 0.01 
M  H 0.01 
R  H 0.01 
I  H 0.01 
T  H 0.01 
N  H 0.01 
E  H 0.01 
S  H 0.01 
L  H 0.01 
G  H 0.01 
I  H 0.96 
L  H 0.01 
K  H 0.01 
G  H 0.69 
Y  H 0.20 
L  H 0.85 
I  H 0.01 
END 
