
PFRMAT AL                                                                        
TARGET T0092                                                                     
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 1VID                                                                      
N  40    V    42                                                                 
I  41    G    43                                                                 
I  42    D    44                                                                 
T  43    A    45                                                                 
A  44    K    46                                                                 
I  45    G    47                                                                 
G  46    Q    48                                                                 
M  47    I    49                                                                 
L  48    M    50                                                                 
A  49    D    51                                                                 
E  50    A    52                                                                 
R  51    V    53                                                                 
F  52    I    54                                                                 
V  53    R    55                                                                 
T  54    E    56                                                                 
A  55    S    58                                                                 
D  56    P    59                                                                 
S  57    S    60                                                                 
N  58    L    61                                                                 
V  59    V    62                                                                 
Y  60    L    63                                                                 
D  61    E    64                                                                 
L  62    L    65                                                                 
G  63    G    66                                                                 
C  64    A    67                                                                 
S  65    Y    68                                                                 
R  66    C    69                                                                 
G  67    G    70                                                                 
A  68    Y    71                                                                 
A  69    S    72                                                                 
T  70    A    73                                                                 
L  71    V    74                                                                 
S  72    R    75                                                                 
A  73    M    76                                                                 
R  74    A    77                                                                 
R  75    R    78                                                                 
I  77    L    79                                                                 
N  78    L    80                                                                 
Q  79    Q    81                                                                 
P  80    P    82                                                                 
N  81    G    83                                                                 
V  82    A    84                                                                 
K  83    R    85                                                                 
I  84    L    86                                                                 
I  85    L    87                                                                 
G  86    T    88                                                                 
I  87    M    89                                                                 
D  88    E    90                                                                 
N  89    M    91                                                                 
S  90    N    92                                                                 
Q  91    P    93                                                                 
P  92    D    94                                                                 
M  93    Y    95                                                                 
V  94    A    96                                                                 
E  95    A    97                                                                 
R  96    I    98                                                                 
C  97    T    99                                                                 
R  98    Q   100                                                                 
Q  99    Q   101                                                                 
H 100    M   102                                                                 
I 101    L   103                                                                 
A 102    N   104                                                                 
A 103    F   105                                                                 
Y 104    A   106                                                                 
H 105    G   107                                                                 
S 106    L   108                                                                 
E 107    Q   109                                                                 
I 108    D   110                                                                 
P 109    K   111                                                                 
V 110    V   112                                                                 
E 111    T   113                                                                 
I 112    I   114                                                                 
L 113    L   115                                                                 
C 114    N   116                                                                 
N 115    G   117                                                                 
D 116    A   118                                                                 
I 117    S   119                                                                 
R 118    Q   120                                                                 
V 120    I   123                                                                 
E 121    P   124                                                                 
I 122    Q   125                                                                 
K 123    L   126                                                                 
N 124    K   127                                                                 
A 125    K   128                                                                 
S 126    K   129                                                                 
M 127    Y   130                                                                 
V 128    D   131                                                                 
I 129    V   132                                                                 
L 130    D   133                                                                 
N 131    T   134                                                                 
F 132    L   135                                                                 
T 133    D   136                                                                 
L 134    M   137                                                                 
Q 135    V   138                                                                 
F 136    F   139                                                                 
L 137    L   140                                                                 
R 142    R   146                                                                 
I 143    Y   147                                                                 
A 144    L   148                                                                 
L 145    P   149                                                                 
L 146    D   150                                                                 
T 147    T   151                                                                 
K 148    L   152                                                                 
I 149    L   153                                                                 
Y 150    L   154                                                                 
G 152    G   158                                                                 
L 153    L   159                                                                 
N 154    L   160                                                                 
P 155    R   161                                                                 
N 156    K   162                                                                 
G 157    G   163                                                                 
V 158    T   164                                                                 
L 159    V   165                                                                 
V 160    L   166                                                                 
L 161    L   167                                                                 
S 162    A   168                                                                 
E 163    D   169                                                                 
K 164    N   170                                                                 
F 165    V   171                                                                 
R 166    I   172                                                                 
F 167    V   173                                                                 
E 168    P   174                                                                 
D 169    G   175                                                                 
N 173    T   176                                                                 
H 174    P   177                                                                 
L 175    D   178                                                                 
L 176    F   179                                                                 
I 177    L   180                                                                 
D 178    A   181                                                                 
L 179    Y   182                                                                 
H 180    V   183                                                                 
H 181    R   184                                                                 
Q 182    G   185                                                                 
Y 189    S   186                                                                 
S 190    S   187                                                                 
E 191    S   188                                                                 
L 192    F   189                                                                 
E 193    E   190                                                                 
V 194    C   191                                                                 
S 195    T   192                                                                 
Q 196    H   193                                                                 
K 197    Y   194                                                                 
R 198    S   195                                                                 
T 199    S   196                                                                 
A 200    Y   197                                                                 
L 201    L   198                                                                 
L 217    E   199                                                                 
K 218    Y   200                                                                 
N 219    M   201                                                                 
V 220    K   202                                                                 
G 221    V   203                                                                 
F 222    V   204                                                                 
S 223    D   205                                                                 
Q 224    G   206                                                                 
V 225    L   207                                                                 
E 226    E   208                                                                 
L 227    K   209                                                                 
W 228    A   210                                                                 
F 229    I   211                                                                 
Q 230    Y   212                                                                 
C 231    Q   213                                                                 
F 232    G   214                                                                 
N 233    P   215                                                                 
F 234    S   216                                                                 
TER                                                                              
END                                                                              


