
PFRMAT AL                                                                        
TARGET T0112                                                                     
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  3                                                                         
PARENT 1YKF_D                                                                    
N   5    M     1                                                                 
L   6    K     2                                                                 
S   7    G     3                                                                 
A   8    F     4                                                                 
V   9    A     5                                                                 
L  10    M     6                                                                 
Y  11    L     7                                                                 
K  12    S     8                                                                 
Q  13    I     9                                                                 
N  14    G    10                                                                 
D  15    K    11                                                                 
L  16    V    12                                                                 
R  17    G    13                                                                 
L  18    W    14                                                                 
E  19    I    15                                                                 
Q  20    E    16                                                                 
R  21    K    17                                                                 
P  22    E    18                                                                 
I  23    K    19                                                                 
P  24    P    20                                                                 
E  25    A    21                                                                 
P  26    P    22                                                                 
K  27    G    23                                                                 
E  28    P    24                                                                 
D  29    F    25                                                                 
E  30    D    26                                                                 
V  31    A    27                                                                 
L  32    I    28                                                                 
L  33    V    29                                                                 
Q  34    R    30                                                                 
M  35    P    31                                                                 
V  38    L    32                                                                 
G  39    A    33                                                                 
I  40    V    34                                                                 
C  41    A    35                                                                 
G  42    P    36                                                                 
S  43    C    37                                                                 
D  44    T    38                                                                 
V  45    S    39                                                                 
H  46    D    40                                                                 
Y  47    T    43                                                                 
Y  48    V    44                                                                 
E  49    F    45                                                                 
H  50    E    46                                                                 
G  51    G    47                                                                 
R  52    A    48                                                                 
I  53    I    49                                                                 
A  54    G    50                                                                 
V  58    E    51                                                                 
K  59    R    52                                                                 
D  60    H    53                                                                 
P  61    N    54                                                                 
M  62    M    55                                                                 
V  63    I    56                                                                 
I  64    L    57                                                                 
G  65    G    58                                                                 
H  66    H    59                                                                 
E  67    E    60                                                                 
A  68    A    61                                                                 
S  69    V    62                                                                 
G  70    G    63                                                                 
T  71    E    64                                                                 
V  72    V    65                                                                 
V  73    V    66                                                                 
K  74    E    67                                                                 
V  75    V    68                                                                 
G  76    G    69                                                                 
K  77    S    70                                                                 
N  78    E    71                                                                 
V  79    V    72                                                                 
K  80    K    73                                                                 
H  81    D    74                                                                 
L  82    F    75                                                                 
K  83    K    76                                                                 
K  84    P    77                                                                 
G  85    G    78                                                                 
D  86    D    79                                                                 
R  87    R    80                                                                 
V  88    V    81                                                                 
A  89    V    82                                                                 
V  90    V    83                                                                 
E  91    P    84                                                                 
P  92    A    85                                                                 
G  93    I    86                                                                 
V  94    T    87                                                                 
P  95    P    88                                                                 
C  96    D    89                                                                 
R  97    W    90                                                                 
R  98    R    91                                                                 
C  99    T    92                                                                 
Q 100    S    93                                                                 
F 101    E    94                                                                 
C 102    V    95                                                                 
K 103    Q    96                                                                 
E 104    R    97                                                                 
G 105    G    98                                                                 
K 106    Y    99                                                                 
Y 107    H   100                                                                 
N 108    Q   101                                                                 
L 109    H   102                                                                 
C 110    S   103                                                                 
P 111    G   104                                                                 
D 112    G   105                                                                 
L 113    M   106                                                                 
T 114    L   107                                                                 
F 115    K   111                                                                 
C 116    F   112                                                                 
A 117    S   113                                                                 
T 118    N   114                                                                 
P 119    V   115                                                                 
P 120    K   116                                                                 
D 121    D   117                                                                 
D 122    G   118                                                                 
G 123    V   119                                                                 
N 124    F   120                                                                 
L 125    G   121                                                                 
A 126    E   122                                                                 
R 127    F   123                                                                 
Y 128    F   124                                                                 
Y 129    H   125                                                                 
V 130    V   126                                                                 
H 131    N   127                                                                 
A 132    D   128                                                                 
A 133    A   129                                                                 
D 134    D   130                                                                 
F 135    N   132                                                                 
C 136    L   133                                                                 
H 137    A   134                                                                 
K 138    H   135                                                                 
L 139    L   136                                                                 
P 140    P   137                                                                 
D 141    K   138                                                                 
N 142    E   139                                                                 
V 143    I   140                                                                 
S 144    P   141                                                                 
A 149    L   142                                                                 
L 150    E   143                                                                 
L 151    A   144                                                                 
E 152    A   145                                                                 
P 153    V   146                                                                 
L 154    M   147                                                                 
S 155    I   148                                                                 
V 156    P   149                                                                 
G 157    D   150                                                                 
V 158    M   151                                                                 
H 159    H   157                                                                 
A 160    G   158                                                                 
C 161    A   159                                                                 
R 162    E   160                                                                 
R 163    L   161                                                                 
A 164    A   162                                                                 
G 165    D   163                                                                 
V 166    I   164                                                                 
Q 167    E   165                                                                 
L 168    L   166                                                                 
G 169    G   167                                                                 
T 170    A   168                                                                 
T 171    T   169                                                                 
V 172    V   170                                                                 
L 173    A   171                                                                 
V 174    V   172                                                                 
I 175    L   173                                                                 
G 176    G   174                                                                 
A 177    I   175                                                                 
G 178    G   176                                                                 
P 179    P   177                                                                 
I 180    V   178                                                                 
G 181    G   179                                                                 
L 182    L   180                                                                 
V 183    M   181                                                                 
S 184    A   182                                                                 
V 185    V   183                                                                 
L 186    A   184                                                                 
A 187    G   185                                                                 
A 188    A   186                                                                 
K 189    K   187                                                                 
A 190    L   188                                                                 
Y 191    R   189                                                                 
G 192    A   191                                                                 
A 193    G   192                                                                 
F 194    R   193                                                                 
V 195    I   194                                                                 
V 196    I   195                                                                 
C 197    A   196                                                                 
T 198    V   197                                                                 
A 199    G   198                                                                 
R 200    S   199                                                                 
S 201    R   200                                                                 
P 202    P   201                                                                 
R 203    V   202                                                                 
R 204    C   203                                                                 
L 205    V   204                                                                 
E 206    D   205                                                                 
V 207    A   206                                                                 
A 208    A   207                                                                 
K 209    K   208                                                                 
N 210    Y   209                                                                 
C 211    Y   210                                                                 
G 212    G   211                                                                 
A 213    A   212                                                                 
D 214    T   213                                                                 
V 215    D   214                                                                 
L 217    I   215                                                                 
V 218    V   216                                                                 
V 219    N   217                                                                 
D 220    Y   218                                                                 
P 221    K   219                                                                 
E 226    D   220                                                                 
S 227    G   221                                                                 
S 228    P   222                                                                 
I 229    I   223                                                                 
I 230    E   224                                                                 
E 231    S   225                                                                 
R 232    Q   226                                                                 
I 233    I   227                                                                 
R 234    M   228                                                                 
S 235    N   229                                                                 
A 236    L   230                                                                 
G 238    T   231                                                                 
D 239    E   232                                                                 
L 240    G   233                                                                 
P 241    K   234                                                                 
N 242    G   235                                                                 
V 243    V   236                                                                 
T 244    D   237                                                                 
I 245    A   238                                                                 
D 246    G   243                                                                 
C 247    G   244                                                                 
S 248    N   245                                                                 
G 249    A   246                                                                 
N 250    D   247                                                                 
E 251    I   248                                                                 
K 252    M   249                                                                 
C 253    I   255                                                                 
I 254    V   256                                                                 
T 255    K   257                                                                 
I 256    P   258                                                                 
G 257    G   259                                                                 
I 258    G   260                                                                 
N 259    T   261                                                                 
I 260    I   262                                                                 
T 261    A   263                                                                 
R 262    N   264                                                                 
T 263    V   265                                                                 
G 264    N   266                                                                 
G 265    Y   267                                                                 
T 266    F   268                                                                 
G 271    G   269                                                                 
M 272    E   270                                                                 
G 273    G   271                                                                 
S 274    E   272                                                                 
Q 275    V   273                                                                 
M 276    L   274                                                                 
V 277    P   275                                                                 
T 278    V   276                                                                 
V 279    P   277                                                                 
P 280    R   278                                                                 
L 281    L   279                                                                 
V 282    E   280                                                                 
N 283    W   281                                                                 
A 284    G   282                                                                 
E 288    C   283                                                                 
I 289    G   284                                                                 
D 290    M   285                                                                 
I 291    A   286                                                                 
K 292    H   287                                                                 
S 293    K   288                                                                 
V 294    T   289                                                                 
F 295    I   290                                                                 
R 296    K   291                                                                 
Y 297    G   292                                                                 
C 298    G   293                                                                 
N 299    L   294                                                                 
D 300    C   295                                                                 
Y 301    P   296                                                                 
P 302    G   297                                                                 
I 303    G   298                                                                 
A 304    R   299                                                                 
L 305    L   300                                                                 
E 306    D   307                                                                 
M 307    L   308                                                                 
V 308    V   309                                                                 
A 309    F   310                                                                 
S 310    Y   311                                                                 
G 311    K   312                                                                 
R 312    R   313                                                                 
C 313    V   314                                                                 
N 314    D   315                                                                 
V 315    P   316                                                                 
K 316    S   317                                                                 
Q 317    K   318                                                                 
L 318    L   319                                                                 
V 319    V   320                                                                 
T 320    T   321                                                                 
H 321    H   322                                                                 
S 322    V   323                                                                 
F 323    F   324                                                                 
K 324    R   325                                                                 
L 325    G   326                                                                 
E 326    F   327                                                                 
Q 327    N   329                                                                 
T 328    I   330                                                                 
V 329    E   331                                                                 
D 330    K   332                                                                 
A 331    A   333                                                                 
F 332    F   334                                                                 
E 333    M   335                                                                 
A 334    L   336                                                                 
A 335    M   337                                                                 
R 336    K   338                                                                 
K 337    D   339                                                                 
K 338    K   340                                                                 
A 339    P   341                                                                 
D 340    D   343                                                                 
N 341    L   344                                                                 
T 342    I   345                                                                 
I 343    K   346                                                                 
K 344    P   347                                                                 
V 345    V   348                                                                 
M 346    V   349                                                                 
I 347    I   350                                                                 
S 348    L   351                                                                 
G 352    A   352                                                                 
TER                                                                              
END                                                                              



