
PFRMAT AL                                                                        
TARGET T0103                                                                     
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.            
METHOD [4] Ralf Thiele and Ralf Zimmer and Thomas Lengauer:                     
METHOD     "Protein Threading by Recursive Dynamic Programming",                
METHOD     JMB,757-779,290,1999                                                 
METHOD [5] Ralf Zimmer and Marko Woehler and Ralf Thiele:                       
METHOD     "New Scoring Schemes for Protein Fold Recognition                    
METHOD     based on Voronoi Contacts",                                          
METHOD     Bioinformatics, 14, 3, 295--308, 1998.                               
METHOD [6] Alexander Zien and Ralf Zimmer and Thomas Lengauer:                  
METHOD     "A simple iterative approach to parameter optimization",             
METHOD     JCB, 2000, in press.                                                 
REMARK =========================================================================
MODEL  1                                                                         
PARENT 1BE6                                                                      
E  12    A     1                                                                 
F  13    Q     2                                                                 
P  14    T     3                                                                 
T  15    V     4                                                                 
I  16    P     5                                                                 
Y  17    Y     6                                                                 
D  18    G     7                                                                 
A  19    I     8                                                                 
S  20    P     9                                                                 
S  21    Q    19                                                                 
A  22    G    20                                                                 
P  23    F    21                                                                 
T  24    K    22                                                                 
A  25    G    23                                                                 
A  26    A    24                                                                 
N  27    N    25                                                                 
T  28    V    26                                                                 
T  29    K    27                                                                 
V  30    V    28                                                                 
G  31    A    29                                                                 
I  32    V    30                                                                 
I  33    L    31                                                                 
I  35    D    32                                                                 
G  36    T    33                                                                 
G  37    G    34                                                                 
V  38    I    35                                                                 
S  39    Q    36                                                                 
Q  40    A    37                                                                 
T  41    S    38                                                                 
L  42    H    39                                                                 
Q  43    P    40                                                                 
D  44    D    41                                                                 
L  45    L    42                                                                 
Q  46    N    43                                                                 
Q  47    V    44                                                                 
Q  60    V    45                                                                 
T  61    G    46                                                                 
I  62    G    47                                                                 
Q  63    A    48                                                                 
T  64    S    49                                                                 
G  65    F    50                                                                 
S  66    V    51                                                                 
S  67    A    52                                                                 
N  68    G    53                                                                 
G  69    E    54                                                                 
D  70    A    55                                                                 
Y  71    Y    57                                                                 
S  72    N    58                                                                 
D  73    T    59                                                                 
D  74    D    60                                                                 
Q  75    G    61                                                                 
Q  76    N    62                                                                 
G  77    G    63                                                                 
Q  78    H    64                                                                 
G  79    G    65                                                                 
E  80    T    66                                                                 
W  81    A    73                                                                 
D  82    A    74                                                                 
L  83    L    75                                                                 
D  84    D    76                                                                 
S  85    N    77                                                                 
Q  86    T    78                                                                 
S  87    T    79                                                                 
I  88    G    80                                                                 
V  89    V    81                                                                 
G  90    L    82                                                                 
S  91    G    83                                                                 
A  92    V    84                                                                 
G  93    A    85                                                                 
G  94    P    86                                                                 
A  95    S    87                                                                 
V  96    V    88                                                                 
Q  97    S    89                                                                 
Q  98    L    90                                                                 
L  99    Y    91                                                                 
L 100    A    92                                                                 
F 101    V    93                                                                 
Y 102    K    94                                                                 
M 103    V    95                                                                 
A 104    L    96                                                                 
D 105    N    97                                                                 
Q 106    S    98                                                                 
S 107    S    99                                                                 
A 108    G   100                                                                 
S 109    S   101                                                                 
G 110    G   102                                                                 
N 111    S   103                                                                 
T 112    S   105                                                                 
G 113    G   106                                                                 
L 114    I   107                                                                 
T 115    V   108                                                                 
Q 116    S   109                                                                 
A 117    G   110                                                                 
F 118    I   111                                                                 
N 119    E   112                                                                 
Q 120    W   113                                                                 
A 121    A   114                                                                 
V 122    T   115                                                                 
S 123    T   116                                                                 
N 125    N   117                                                                 
V 126    G   118                                                                 
A 127    M   119                                                                 
K 128    D   120                                                                 
V 129    V   121                                                                 
I 130    I   122                                                                 
N 131    N   123                                                                 
V 132    M   124                                                                 
S 133    S   125                                                                 
L 134    L   126                                                                 
G 135    G   127                                                                 
W 136    G   128                                                                 
C 137    A   129                                                                 
E 138    S   130                                                                 
A 139    G   131                                                                 
D 140    S   132                                                                 
A 141    T   133                                                                 
G 145    A   134                                                                 
T 146    M   135                                                                 
L 147    K   136                                                                 
Q 148    Q   137                                                                 
A 149    A   138                                                                 
E 150    V   139                                                                 
D 151    D   140                                                                 
R 152    N   141                                                                 
I 153    A   142                                                                 
F 154    Y   143                                                                 
A 155    A   144                                                                 
Q 160    R   145                                                                 
G 161    G   146                                                                 
Q 162    V   147                                                                 
T 163    V   148                                                                 
F 164    V   149                                                                 
S 165    V   150                                                                 
V 166    A   151                                                                 
S 167    A   152                                                                 
S 168    A   153                                                                 
G 169    G   154                                                                 
D 170    N   155                                                                 
E 171    S   156                                                                 
G 172    G   157                                                                 
P 182    N   158                                                                 
D 183    S   159                                                                 
G 184    G   160                                                                 
S 185    S   161                                                                 
T 186    T   162                                                                 
Y 187    N   163                                                                 
S 188    T   164                                                                 
V 189    I   165                                                                 
S 190    G   166                                                                 
W 191    Y   167                                                                 
P 192    P   168                                                                 
A 193    A   169                                                                 
S 194    K   170                                                                 
S 195    Y   171                                                                 
P 196    D   172                                                                 
N 197    S   173                                                                 
V 198    V   174                                                                 
I 199    I   175                                                                 
A 200    A   176                                                                 
V 201    V   177                                                                 
G 202    G   178                                                                 
G 203    A   179                                                                 
Y 214    V   180                                                                 
S 215    D   181                                                                 
N 216    S   182                                                                 
E 217    N   183                                                                 
T 218    S   184                                                                 
V 219    N   185                                                                 
W 220    R   186                                                                 
N 221    A   187                                                                 
E 222    S   188                                                                 
G 223    F   189                                                                 
L 224    S   190                                                                 
D 225    S   191                                                                 
S 226    V   192                                                                 
N 227    G   193                                                                 
G 228    A   194                                                                 
K 229    E   195                                                                 
L 230    L   196                                                                 
W 231    E   197                                                                 
A 232    V   198                                                                 
T 233    M   199                                                                 
G 234    A   200                                                                 
G 235    P   201                                                                 
G 236    G   202                                                                 
Y 237    A   203                                                                 
S 238    G   204                                                                 
V 239    V   205                                                                 
Y 240    Y   206                                                                 
E 241    S   207                                                                 
S 242    T   208                                                                 
S 251    Y   209                                                                 
G 252    P   210                                                                 
T 253    T   211                                                                 
P 254    N   212                                                                 
G 255    T   213                                                                 
R 256    Y   214                                                                 
R 257    A   215                                                                 
L 258    T   216                                                                 
L 259    L   217                                                                 
P 260    N   218                                                                 
D 261    G   219                                                                 
I 262    T   220                                                                 
S 263    S   221                                                                 
F 264    M   222                                                                 
D 265    A   223                                                                 
A 266    S   224                                                                 
A 267    P   225                                                                 
Q 268    H   226                                                                 
G 269    V   227                                                                 
T 270    A   230                                                                 
G 271    A   231                                                                 
A 272    A   232                                                                 
L 273    L   233                                                                 
I 274    I   234                                                                 
Y 275    L   235                                                                 
N 276    S   236                                                                 
Q 282    K   237                                                                 
I 283    H   238                                                                 
G 284    P   239                                                                 
G 285    N   240                                                                 
T 286    L   241                                                                 
S 287    S   242                                                                 
L 288    A   243                                                                 
A 289    S   244                                                                 
G 295    Q   245                                                                 
L 296    V   246                                                                 
W 297    R   247                                                                 
A 298    N   248                                                                 
R 299    R   249                                                                 
L 300    L   250                                                                 
Q 301    S   251                                                                 
S 302    S   252                                                                 
S 307    T   253                                                                 
L 308    A   254                                                                 
G 309    T   255                                                                 
F 310    Y   256                                                                 
P 311    L   257                                                                 
A 312    G   258                                                                 
A 313    S   259                                                                 
S 314    S   260                                                                 
F 315    F   261                                                                 
Y 316    Y   262                                                                 
S 317    Y   263                                                                 
T 322    G   264                                                                 
P 323    K   265                                                                 
S 324    G   266                                                                 
L 325    L   267                                                                 
V 326    I   268                                                                 
H 327    N   269                                                                 
D 328    V   270                                                                 
V 329    E   271                                                                 
K 330    A   272                                                                 
S 331    A   273                                                                 
G 332    A   274                                                                 
N 333    Q   275                                                                 
TER                                                                              
END                                                                              



