
PFRMAT AL                                                                        
TARGET T0093                                                                     
REMARK =========================================================================
AUTHOR 6923-1755-6564                                                           
REMARK Ralf Zimmer, GMD-SCAI,                                                   
REMARK Theo Mevissen, GMD-SCAI,                                                 
REMARK Ingolf Sommer, GMD-SCAI,                                                 
REMARK Thomas Lengauer, GMD-SCAI,                                               
REMARK German National Research Center for Information Technology               
REMARK Institute for Algorithms and Scientific Computing                        
REMARK =========================================================================
METHOD A reduced candidate list is produced via ToPLign [1]                     
METHOD sequence/profile alignments, 123D [2] and RDP [3].                       
METHOD The top scoring candidates from this list and the                        
METHOD corresponding refined alignments have been produced                      
METHOD with RDP [3] using newly derived modifications of                        
METHOD contact capacity [2] and pair interaction potentials.                    
METHOD References:                                                              
METHOD [1] Heinz Mevissen and Ralf Thiele and Ralf Zimmer and Thomas Lengauer:  
METHOD     "Analysis of Protein Alignments -- The software environment ToPLign",
METHOD     GMD, 1994-98.                                                        
METHOD [2] Nick Alexandrov and Ruth Nussinov and Ralf Zimmer:                   
METHOD     "Fast Protein Fold Recognition via Sequence to Structure Alignment   
METHOD     and Contact Capacity Potentials",                                    
METHOD     Pacific Symposium on Biocomputing'96, World Scientific Publ. Co.,    
METHOD     1996, 53--72.                                                        
METHOD [3] Ralf Thiele and Ralf Zimmer and Thomas Lengauer:                     
METHOD     "Recursive Dynamic Programming for Adaptive Sequence                 
METHOD     and Structure Alignment",                                            
METHOD     ISMB'95, C. Rawlings et al. (Eds.), AAAI Press, 384--392.            
REMARK =========================================================================
MODEL  1                                                                         
PARENT 1COZ_A                                                                    
M   1    M     1                                                                 
L   2    K     2                                                                 
D   3    K     3                                                                 
I   4    V     4                                                                 
V   5    I     5                                                                 
L   6    T     6                                                                 
Y   7    Y     7                                                                 
E   8    G     8                                                                 
P   9    D    11                                                                 
E  10    L    12                                                                 
I  11    L    13                                                                 
P  12    H    14                                                                 
Q  13    W    15                                                                 
N  14    G    16                                                                 
T  15    H    17                                                                 
G  16    I    18                                                                 
N  17    K    19                                                                 
I  18    L    20                                                                 
I  19    L    21                                                                 
R  20    E    22                                                                 
L  21    R    23                                                                 
C  22    A    24                                                                 
A  23    K    25                                                                 
N  24    Q    26                                                                 
T  25    L    27                                                                 
G  26    G    28                                                                 
R  28    D    29                                                                 
L  29    Y    30                                                                 
H  30    L    31                                                                 
L  31    V    32                                                                 
I  32    V    33                                                                 
E  33    A    34                                                                 
P  34    I    35                                                                 
L  35    S    36                                                                 
G  36    T    37                                                                 
F  37    D    38                                                                 
T  38    E    39                                                                 
W  39    F    40                                                                 
D  40    N    41                                                                 
D  41    L    42                                                                 
K  42    Q    43                                                                 
R  43    K    44                                                                 
L  44    Q    45                                                                 
R  45    K    46                                                                 
R  46    K    47                                                                 
S  47    A    48                                                                 
G  48    Y    49                                                                 
L  49    H    50                                                                 
D  50    S    51                                                                 
Y  51    Y    52                                                                 
H  52    E    53                                                                 
E  53    H    54                                                                 
F  54    R    55                                                                 
A  55    K    56                                                                 
E  56    L    57                                                                 
I  57    I    58                                                                 
K  58    L    59                                                                 
R  59    E    60                                                                 
H  60    T    61                                                                 
K  61    I    62                                                                 
T  62    R    63                                                                 
F  63    Y    64                                                                 
K  73    D    66                                                                 
R  74    E    67                                                                 
L  75    V    68                                                                 
F  76    I    69                                                                 
A  77    P    70                                                                 
L  78    E    71                                                                 
T  79    K    72                                                                 
T  80    N    73                                                                 
K  81    W    74                                                                 
G  82    E    75                                                                 
C  83    Q    76                                                                 
A  85    K    77                                                                 
H  86    K    78                                                                 
S  87    Q    79                                                                 
Q  88    D    80                                                                 
V  89    I    81                                                                 
K  90    I    82                                                                 
F  91    D    83                                                                 
K  92    H    84                                                                 
L  93    N    85                                                                 
G  94    I    86                                                                 
D  95    D    87                                                                 
Y  96    V    88                                                                 
L  97    F    89                                                                 
M  98    V    90                                                                 
F  99    M    91                                                                 
G 100    G    92                                                                 
P 101    D    93                                                                 
E 102    D    94                                                                 
T 103    W    95                                                                 
R 104    E    96                                                                 
G 105    G    97                                                                 
E 117    C   106                                                                 
Q 118    E   107                                                                 
K 119    V   108                                                                 
I 120    V   109                                                                 
R 121    Y   110                                                                 
I 122    L   111                                                                 
P 123    P   112                                                                 
M 124    R   113                                                                 
T 125    T   114                                                                 
A 126    E   115                                                                 
N 127    G   116                                                                 
V 139    I   117                                                                 
T 140    S   118                                                                 
V 141    T   119                                                                 
Y 142    T   120                                                                 
E 143    K   121                                                                 
A 144    I   122                                                                 
W 145    K   123                                                                 
R 146    E   124                                                                 
Q 147    E   125                                                                 
L 148    I   126                                                                 
TER                                                                              
END                                                                              



