
PFRMAT AL                                                                        
TARGET T0089                                                                     
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 1DKG_D                                                                    
M   1    K     3                                                                 
I   2    I     4                                                                 
D   3    D     8                                                                 
L   4    L     9                                                                 
S   5    G    10                                                                 
K   6    T    11                                                                 
T   7    T    12                                                                 
V   8    N    13                                                                 
F   9    S    14                                                                 
Y  10    C    15                                                                 
T  11    V    16                                                                 
S  12    A    17                                                                 
I  13    I    18                                                                 
D  14    M    19                                                                 
I  15    D    20                                                                 
G  16    G    21                                                                 
S  17    T    22                                                                 
R  18    T    23                                                                 
G  22    P    24                                                                 
L  23    R    25                                                                 
V  24    V    26                                                                 
L  25    L    27                                                                 
G  26    E    28                                                                 
K  27    N    29                                                                 
R  28    A    30                                                                 
D  29    E    31                                                                 
Q  30    G    32                                                                 
E  31    D    33                                                                 
W  32    R    34                                                                 
E  33    T    35                                                                 
A  34    T    36                                                                 
K  51    P    37                                                                 
D  52    S    38                                                                 
A  53    I    39                                                                 
I  54    I    40                                                                 
A  55    A    41                                                                 
F  56    Y    42                                                                 
K  57    T    43                                                                 
E  58    Q    44                                                                 
S  59    D    45                                                                 
V  60    G    46                                                                 
N  61    E    47                                                                 
T  62    T    48                                                                 
L  63    L    49                                                                 
L  64    V    50                                                                 
K  65    G    51                                                                 
E  66    Q    52                                                                 
L  67    P    53                                                                 
E  68    A    54                                                                 
E  69    K    55                                                                 
Q  70    R    56                                                                 
L  71    Q    57                                                                 
Q  72    A    58                                                                 
K  73    V    59                                                                 
S  74    T    60                                                                 
L  75    N    61                                                                 
R  76    P    62                                                                 
S  77    Q    63                                                                 
D  78    N    64                                                                 
F  79    T    65                                                                 
V  80    L    66                                                                 
I  81    F    67                                                                 
S  82    A    68                                                                 
F  83    I    69                                                                 
S  84    K    70                                                                 
S  85    G    74                                                                 
V  86    R    75                                                                 
S  87    R    76                                                                 
F  88    F    77                                                                 
E  89    Q    78                                                                 
R  90    D    79                                                                 
E  91    E    80                                                                 
V  94    E    81                                                                 
I  95    V    82                                                                 
E  96    Q    83                                                                 
R  97    R    84                                                                 
D  98    D    85                                                                 
K 103    V    86                                                                 
R 104    S    87                                                                 
S 105    I    88                                                                 
I 106    M    89                                                                 
T 107    P    90                                                                 
L 108    F    91                                                                 
D 109    K    92                                                                 
I 110    I    93                                                                 
L 111    I    94                                                                 
S 112    A    95                                                                 
E 113    A    96                                                                 
M 114    D    97                                                                 
Q 115    N    98                                                                 
S 116    G    99                                                                 
E 117    D   100                                                                 
A 118    A   101                                                                 
L 119    W   102                                                                 
E 120    V   103                                                                 
K 121    E   104                                                                 
L 122    V   105                                                                 
K 123    K   106                                                                 
E 124    G   107                                                                 
N 125    Q   108                                                                 
G 126    K   109                                                                 
K 127    M   110                                                                 
T 128    A   111                                                                 
P 129    P   112                                                                 
L 130    P   113                                                                 
H 131    Q   114                                                                 
I 132    I   115                                                                 
F 133    S   116                                                                 
S 134    A   117                                                                 
Y 137    E   118                                                                 
L 138    V   119                                                                 
L 139    L   120                                                                 
D 140    K   121                                                                 
D 141    K   122                                                                 
A 153    M   123                                                                 
S 154    K   124                                                                 
K 155    K   125                                                                 
I 156    T   126                                                                 
A 157    A   127                                                                 
I 158    E   128                                                                 
E 159    D   129                                                                 
Y 160    Y   130                                                                 
T 161    T   136                                                                 
S 162    E   137                                                                 
I 163    A   138                                                                 
V 164    V   139                                                                 
V 165    I   140                                                                 
P 166    T   141                                                                 
L 167    V   142                                                                 
K 168    P   143                                                                 
M 172    A   144                                                                 
F 173    Y   145                                                                 
Y 174    F   146                                                                 
N 175    N   147                                                                 
F 176    D   148                                                                 
L 177    A   149                                                                 
Q 178    R   151                                                                 
D 179    Q   152                                                                 
T 180    A   153                                                                 
V 181    T   154                                                                 
K 182    K   155                                                                 
S 183    D   156                                                                 
P 184    A   157                                                                 
F 185    L   163                                                                 
Q 186    E   164                                                                 
L 187    V   165                                                                 
K 188    K   166                                                                 
S 189    R   167                                                                 
S 190    I   168                                                                 
L 191    I   169                                                                 
V 192    N   170                                                                 
S 193    E   171                                                                 
T 194    P   172                                                                 
A 195    T   173                                                                 
E 196    A   174                                                                 
G 197    A   175                                                                 
V 198    A   176                                                                 
L 199    L   177                                                                 
T 200    A   178                                                                 
T 201    K   183                                                                 
E 203    T   185                                                                 
K 204    G   186                                                                 
D 205    N   187                                                                 
R 206    R   188                                                                 
G 207    T   189                                                                 
V 208    I   190                                                                 
V 209    A   191                                                                 
V 210    V   192                                                                 
V 211    Y   193                                                                 
N 212    D   194                                                                 
L 213    L   195                                                                 
G 214    G   196                                                                 
Y 215    G   198                                                                 
N 216    T   199                                                                 
F 217    F   200                                                                 
T 218    D   201                                                                 
G 219    I   202                                                                 
L 220    S   203                                                                 
I 221    I   204                                                                 
A 222    I   205                                                                 
Y 223    E   206                                                                 
K 224    I   207                                                                 
N 225    D   208                                                                 
G 226    E   209                                                                 
I 231    K   214                                                                 
S 232    T   215                                                                 
Y 233    F   216                                                                 
V 234    E   217                                                                 
P 235    V   218                                                                 
V 236    L   219                                                                 
G 237    G   228                                                                 
M 238    G   229                                                                 
K 239    E   230                                                                 
H 240    D   231                                                                 
V 241    F   232                                                                 
I 242    D   233                                                                 
K 243    S   234                                                                 
D 244    R   235                                                                 
V 245    L   236                                                                 
S 246    I   237                                                                 
A 247    N   238                                                                 
V 248    Y   239                                                                 
L 249    L   240                                                                 
D 250    V   241                                                                 
T 251    E   242                                                                 
S 252    E   243                                                                 
F 253    F   244                                                                 
E 254    K   245                                                                 
E 255    K   246                                                                 
S 256    D   247                                                                 
E 257    Q   248                                                                 
R 258    G   249                                                                 
L 259    I   250                                                                 
I 260    D   251                                                                 
I 261    L   252                                                                 
T 262    R   253                                                                 
H 263    N   254                                                                 
G 264    D   255                                                                 
N 265    P   256                                                                 
A 266    L   257                                                                 
V 267    A   258                                                                 
Y 268    M   259                                                                 
N 269    Q   260                                                                 
D 270    R   261                                                                 
L 271    L   262                                                                 
K 272    K   263                                                                 
E 273    E   264                                                                 
E 274    A   265                                                                 
E 275    A   266                                                                 
I 276    E   267                                                                 
Q 277    K   270                                                                 
Y 278    I   271                                                                 
R 279    E   272                                                                 
G 280    L   273                                                                 
L 281    S   274                                                                 
D 282    S   275                                                                 
G 283    A   276                                                                 
N 284    Q   277                                                                 
T 285    Q   278                                                                 
I 286    T   279                                                                 
K 287    D   280                                                                 
T 288    A   290                                                                 
T 289    T   291                                                                 
T 290    G   292                                                                 
A 291    P   293                                                                 
K 292    K   294                                                                 
K 293    H   295                                                                 
L 294    M   296                                                                 
S 295    N   297                                                                 
V 296    I   298                                                                 
I 297    K   299                                                                 
I 298    V   300                                                                 
H 299    T   301                                                                 
A 300    A   303                                                                 
R 301    K   304                                                                 
L 302    L   305                                                                 
R 303    E   306                                                                 
E 304    S   307                                                                 
I 305    L   312                                                                 
M 306    V   313                                                                 
S 307    N   314                                                                 
K 308    R   315                                                                 
S 309    S   316                                                                 
K 310    I   317                                                                 
K 311    E   318                                                                 
F 312    L   319                                                                 
F 313    L   320                                                                 
R 314    K   321                                                                 
E 315    V   322                                                                 
V 316    A   323                                                                 
V 321    L   324                                                                 
E 322    Q   325                                                                 
E 323    D   326                                                                 
G 324    A   327                                                                 
E 325    G   328                                                                 
I 326    L   329                                                                 
G 327    S   330                                                                 
I 328    V   331                                                                 
P 329    S   332                                                                 
G 330    D   335                                                                 
G 331    D   336                                                                 
V 332    V   337                                                                 
V 333    I   338                                                                 
L 334    L   339                                                                 
T 335    V   340                                                                 
G 336    G   341                                                                 
G 337    G   342                                                                 
G 338    Q   343                                                                 
A 339    T   344                                                                 
K 340    R   345                                                                 
I 341    M   346                                                                 
P 342    P   347                                                                 
R 343    M   348                                                                 
I 344    V   349                                                                 
N 345    Q   350                                                                 
E 346    K   351                                                                 
L 347    K   352                                                                 
A 348    V   353                                                                 
T 349    A   354                                                                 
E 350    E   355                                                                 
V 351    F   356                                                                 
F 352    F   357                                                                 
K 353    G   358                                                                 
S 354    K   359                                                                 
P 355    E   360                                                                 
V 356    P   361                                                                 
R 357    R   362                                                                 
S 368    K   363                                                                 
I 369    D   364                                                                 
I 370    V   365                                                                 
N 371    N   366                                                                 
A 372    P   367                                                                 
D 373    D   368                                                                 
E 374    E   369                                                                 
V 375    A   370                                                                 
P 379    V   371                                                                 
S 380    A   372                                                                 
F 381    I   373                                                                 
A 382    G   374                                                                 
A 383    A   375                                                                 
A 384    A   376                                                                 
F 385    Q   378                                                                 
G 386    G   379                                                                 
N 387    G   380                                                                 
V 388    V   381                                                                 
F 389    L   382                                                                 
A 390    T   383                                                                 
TER                                                                              
END                                                                              



