PFRMAT AL 
TARGET T0048 
AUTHOR 5827-4749-3439 
METHOD T0048 structure prediction 
METHOD 
METHOD As usual, we employed a two-pronged approach: (1) We scored the  
METHOD target against all the HMMs and threading models in our libraries,  
METHOD and (2) we gathered homologs to the target using PsiBLAST,  
METHOD constructed an HMM for the target and homologs (using UCSC's HMM  
METHOD software), and scored PDB.  
METHOD This yielded three sets of scores, which we then used  
METHOD to find a target-structure match. 
METHOD  
METHOD The highest-scoring HMM in the first stage of the analysis  
METHOD was constructed for the scop domain d1dcoh and homologs. 
METHOD In fact, the target was one of the homologs in the set! 
METHOD The HMM constructed for the target and homologs in the 
METHOD second stage also scored this structure in first place. 
METHOD 
METHOD The alignment submitted was created by aligning the target  
METHOD and structure to the subfamily HMM constructed for the  
METHOD domain d1dcoh (unpublished method). The alignment is 
METHOD unaltered. 
METHOD 
MODEL 1 
PARENT 1dco_H 
R    13    H    6 
A    14    R    7 
V    19    L    8 
S    20    S    9 
D    21    A    10 
E    22    E    11 
E    23    E    12 
L    24    R    13 
P    25    D    14 
V    26    Q    15 
L    27    L    16 
L    28    L    17 
R    29    P    18 
Q    30    N    19 
I    31    L    20 
P    32    R    21 
D    33    G    24 
W    34    W    25 
N    35    N    26 
I    36    L    28 
E    37    E    29 
V    38    G    30 
R    39    R    31 
D    40    D    32 
G    41    A    33 
I    42    I    34 
M    43    F    35 
K    47    K    36 
V    48    Q    37 
Y    49    F    38 
L    50    H    39 
F    51    F    40 
K    52    K    41 
N    53    D    42 
F    54    F    43 
K    55    N    44 
H    56    R    45 
A    57    A    46 
L    58    F    47 
A    59    G    48 
F    60    F    49 
T    61    M    50 
N    62    T    51 
A    63    R    52 
V    64    V    53 
G    65    A    54 
E    66    L    55 
I    67    Q    56 
S    68    A    57 
E    69    E    58 
A    70    K    59 
E    71    L    60 
G    72    D    61 
H    73    H    62 
H    74    H    63 
P    75    P    64 
G    76    E    65 
L    77    W    66 
L    78    F    67 
T    79    N    68 
E    80    V    69 
W    81    Y    70 
G    82    N    71 
K    83    K    72 
V    84    V    73 
T    85    H    74 
V    86    I    75 
T    87    T    76 
W    88    L    77 
W    89    S    78 
S    90    T    79 
H    91    H    80 
S    92    E    81 
I    93    C    82 
K    94    A    83 
G    95    G    84 
L    96    L    85 
H    97    S    86 
R    98    E    87 
N    99    R    88 
D    100    D    89 
F    101    I    90 
I    102    N    91 
M    103    L    92 
A    104    A    93 
A    105    S    94 
R    106    F    95 
T    107    I    96 
D    108    E    97 
E    109    Q    98 
V    110    V    99 
A    111    A    100 
K    112    V    101 
T    113    S    102 
A    114    M    103 
TER 
END 
