PFRMAT AL                                                               
TARGET T0053                                                            
REMARK ================================================================ 
AUTHOR 5601-8785-5692                                                   
REMARK Gudrun Lange, HMR AG,                                            
REMARK Heinz Mevissen, GMD,                                             
REMARK Ralf Thiele, GMD,                                                
REMARK Ralf Zimmer, GMD,                                                
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 1TRE_B                                                                     
M      1    M      3                                                       
K      2    R      4                                                       
K      3    H      5                                                       
A      4    P      6                                                       
L      5    L      7                                                       
L      6    V      8                                                       
V      7    M      9                                                       
V      8    G     10                                                       
S      9    N     11                                                       
F     10    W     12                                                       
G     11    K     13                                                       
T     12    L     14                                                       
S     13    N     15                                                       
Y     14    S     17                                                       
H     15    R     18                                                       
D     16    H     19                                                       
T     17    M     20                                                       
C     18    V     21                                                       
E     19    H     22                                                       
K     20    E     23                                                       
N     21    L     24                                                       
I     22    V     25                                                       
V     23    S     26                                                       
A     24    N     27                                                       
C     25    L     28                                                       
E     26    R     29                                                       
R     27    K     30                                                       
D     28    E     31                                                       
L     29    L     32                                                       
A     30    A     33                                                       
A     31    G     34                                                       
R     36    V     35                                                       
D     37    A     36                                                       
L     38    G     37                                                       
F     39    C     38                                                       
R     40    A     39                                                       
A     41    V     40                                                       
F     42    A     41                                                       
T     43    I     42                                                       
S     44    A     43                                                       
G     45    E     46                                                       
M     46    M     47                                                       
I     47    Y     48                                                       
I     48    I     49                                                       
R     49    D     50                                                       
K     50    M     51                                                       
L     51    A     52                                                       
R     52    K     53                                                       
Q     53    R     54                                                       
R     54    E     55                                                       
D     55    A     56                                                       
G     56    M     62                                                       
I     57    L     63                                                       
D     58    G     64                                                       
I     59    A     65                                                       
D     60    Q     66                                                       
T     61    N     67                                                       
P     62    V     68                                                       
L     63    E     79                                                       
Q     64    T     80                                                       
A     65    S     81                                                       
L     66    A     82                                                       
Q     67    A     83                                                       
K     68    M     84                                                       
L     69    L     85                                                       
A     70    K     86                                                       
A     71    D     87                                                       
Q     72    I     88                                                       
G     73    G     89                                                       
Y     74    A     90                                                       
Q     75    Q     91                                                       
D     76    Y     92                                                       
V     77    I     93                                                       
A     78    I     94                                                       
I     79    I     95                                                       
Q     80    S     98                                                       
S     81    E     99                                                       
L     82    R    100                                                       
H     83    R    101                                                       
I     84    T    102                                                       
I     85    Y    103                                                       
N     86    H    104                                                       
G     87    K    105                                                       
D     88    E    106                                                       
E     89    S    107                                                       
Y     90    D    108                                                       
E     91    E    109                                                       
K     92    L    110                                                       
I     93    I    111                                                       
V     94    A    112                                                       
R     95    K    113                                                       
E     96    K    114                                                       
V     97    F    115                                                       
Q     98    A    116                                                       
L     99    V    117                                                       
L    100    L    118                                                       
R    101    K    119                                                       
P    102    E    120                                                       
L    103    L    123                                                       
F    104    T    124                                                       
T    105    P    125                                                       
R    106    V    126                                                       
L    107    L    127                                                       
T    108    C    128                                                       
L    109    I    129                                                       
G    110    G    130                                                       
V    111    E    131                                                       
P    112    T    132                                                       
L    113    E    133                                                       
L    114    A    134                                                       
S    115    E    135                                                       
S    116    N    136                                                       
H    117    E    137                                                       
N    118    E    143                                                       
D    119    V    144                                                       
Y    120    C    145                                                       
V    121    A    146                                                       
Q    122    R    147                                                       
L    123    Q    148                                                       
M    124    I    149                                                       
Q    125    D    150                                                       
A    126    A    151                                                       
L    127    V    152                                                       
R    128    L    153                                                       
Q    129    K    154                                                       
Q    130    T    155                                                       
M    131    Q    156                                                       
P    132    G    157                                                       
L    134    A    158                                                       
R    135    A    159                                                       
Q    136    A    160                                                       
T    137    F    161                                                       
E    138    E    162                                                       
K    139    A    164                                                       
V    140    V    165                                                       
V    141    I    166                                                       
F    142    A    167                                                       
M    143    Y    168                                                       
G    144    E    169                                                       
H    145    T    176                                                       
G    146    G    177                                                       
A    147    K    178                                                       
S    148    S    179                                                       
H    149    A    180                                                       
H    150    T    181                                                       
A    151    P    182                                                       
F    152    A    183                                                       
A    153    Q    184                                                       
A    154    A    185                                                       
Y    155    Q    186                                                       
A    156    A    187                                                       
C    157    V    188                                                       
L    158    H    189                                                       
D    159    K    190                                                       
H    160    F    191                                                       
M    161    I    192                                                       
M    162    R    193                                                       
T    163    D    194                                                       
A    164    H    195                                                       
Q    165    I    196                                                       
R    166    A    197                                                       
F    167    K    198                                                       
P    199    Q    206                                                       
L    200    V    207                                                       
M    201    I    208                                                       
L    202    I    209                                                       
V    203    Q    210                                                       
A    204    Y    211                                                       
G    205    G    212                                                       
D    206    G    213                                                       
D    211    S    214                                                       
M    212    V    215                                                       
A    213    N    216                                                       
S    214    A    217                                                       
D    215    S    218                                                       
S    219    N    219                                                       
W    220    A    220                                                       
K    221    A    221                                                       
M    222    E    222                                                       
R    223    L    223                                                       
F    224    F    224                                                       
N    225    A    225                                                       
A    226    Q    226                                                       
A    227    P    227                                                       
G    228    D    228                                                       
I    229    I    229                                                       
P    230    D    230                                                       
T    232    G    231                                                       
P    233    A    232                                                       
W    234    L    233                                                       
L    235    V    234                                                       
S    236    G    235                                                       
G    237    G    236                                                       
L    238    A    237                                                       
G    239    S    238                                                       
E    240    L    239                                                       
N    241    K    240                                                       
P    242    A    241                                                       
A    243    D    242                                                       
I    244    A    243                                                       
R    245    F    244                                                       
A    246    A    245                                                       
M    247    V    246                                                       
F    248    I    247                                                       
V    249    V    248                                                       
A    250    K    249                                                       
H    251    A    250                                                       
L    252    A    251                                                       
H    253    E    252                                                       
Q    254    A    253                                                       
A    255    A    254                                                       
L    256    K    255                                                       
TER                                                                     
END                                                                     
