
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  2                                                                         
PARENT 1QCX_A                                                                    
Q  86    A     1                                                                 
S  87    G     2                                                                 
I  88    V     3                                                                 
V  89    V     4                                                                 
G  90    G     5                                                                 
S  91    A     6                                                                 
A  92    A     7                                                                 
G  93    E     8                                                                 
G  94    G     9                                                                 
A  95    F    10                                                                 
V  96    T    28                                                                 
Q  97    D    29                                                                 
Q  98    E    30                                                                 
L  99    L    31                                                                 
L 100    V    32                                                                 
F 101    S    33                                                                 
Y 102    Y    34                                                                 
M 103    L    35                                                                 
A 104    G    36                                                                 
D 105    D    37                                                                 
Q 106    N    38                                                                 
S 107    E    39                                                                 
A 108    P    40                                                                 
G 110    R    41                                                                 
N 111    V    42                                                                 
T 112    I    43                                                                 
G 113    I    44                                                                 
L 114    L    45                                                                 
T 115    D    46                                                                 
Q 116    Q    47                                                                 
A 117    T    48                                                                 
F 118    F    49                                                                 
N 119    D    50                                                                 
Q 120    F    51                                                                 
A 121    T    52                                                                 
V 122    G    53                                                                 
S 123    T    54                                                                 
D 124    E    55                                                                 
N 125    G    56                                                                 
V 126    T    57                                                                 
A 127    E    58                                                                 
K 128    T    59                                                                 
V 129    Q    73                                                                 
I 130    V    74                                                                 
N 131    A    75                                                                 
V 132    I    76                                                                 
S 133    N    77                                                                 
L 134    H    79                                                                 
G 135    S    80                                                                 
W 136    W    81                                                                 
C 137    C    82                                                                 
E 138    D    83                                                                 
A 139    N    84                                                                 
D 140    Y    85                                                                 
A 141    Q    86                                                                 
N 142    A    87                                                                 
A 143    S    88                                                                 
D 144    A    89                                                                 
G 145    P    90                                                                 
T 146    K    91                                                                 
L 147    V    92                                                                 
R 152    S    93                                                                 
I 153    V    94                                                                 
F 154    T    95                                                                 
A 155    Y    96                                                                 
T 156    D    97                                                                 
A 157    K    98                                                                 
A 158    A    99                                                                 
A 159    V   106                                                                 
Q 160    N   107                                                                 
G 161    S   108                                                                 
Q 162    N   109                                                                 
T 163    K   110                                                                 
F 164    S   111                                                                 
S 165    I   112                                                                 
V 166    V   113                                                                 
S 167    G   114                                                                 
S 168    Q   115                                                                 
G 169    G   116                                                                 
D 170    T   117                                                                 
E 171    K   118                                                                 
G 172    G   119                                                                 
V 173    V   120                                                                 
Y 174    I   121                                                                 
E 175    K   122                                                                 
C 176    G   123                                                                 
N 177    K   124                                                                 
N 178    G   125                                                                 
R 179    L   126                                                                 
G 180    R   127                                                                 
Y 181    V   128                                                                 
P 182    V   129                                                                 
D 183    S   130                                                                 
G 184    G   131                                                                 
S 185    A   132                                                                 
T 186    K   133                                                                 
Y 187    N   134                                                                 
S 188    V   135                                                                 
V 189    I   136                                                                 
S 190    I   137                                                                 
W 191    Q   138                                                                 
P 192    N   139                                                                 
A 193    D   144                                                                 
S 194    I   145                                                                 
S 195    N   146                                                                 
P 196    P   147                                                                 
N 197    K   148                                                                 
V 198    Y   149                                                                 
I 199    V   150                                                                 
A 200    W   151                                                                 
V 201    G   152                                                                 
G 202    G   153                                                                 
G 203    D   154                                                                 
T 204    A   155                                                                 
T 205    I   156                                                                 
L 206    T   157                                                                 
Y 207    V   158                                                                 
T 208    D   159                                                                 
T 209    D   160                                                                 
N 216    S   161                                                                 
E 217    D   162                                                                 
T 218    L   163                                                                 
V 219    V   164                                                                 
W 220    W   165                                                                 
N 221    I   166                                                                 
E 222    D   167                                                                 
G 223    H   168                                                                 
L 224    I   174                                                                 
D 225    G   175                                                                 
S 226    R   176                                                                 
N 227    Q   177                                                                 
G 228    H   178                                                                 
K 229    I   179                                                                 
L 230    V   180                                                                 
W 231    L   181                                                                 
A 232    G   182                                                                 
T 233    T   183                                                                 
G 234    S   184                                                                 
G 235    A   185                                                                 
G 236    S   192                                                                 
Y 237    Y   193                                                                 
S 238    S   194                                                                 
V 239    L   195                                                                 
Y 240    I   196                                                                 
E 241    D   197                                                                 
S 242    G   198                                                                 
K 243    R   199                                                                 
P 244    S   200                                                                 
S 245    D   201                                                                 
W 246    Y   202                                                                 
Q 247    G   213                                                                 
S 248    V   214                                                                 
V 249    Y   215                                                                 
V 250    L   216                                                                 
S 251    D   217                                                                 
G 252    G   218                                                                 
T 253    S   219                                                                 
P 254    N   220                                                                 
G 255    D   221                                                                 
R 256    M   222                                                                 
R 257    V   223                                                                 
L 258    T   224                                                                 
L 259    L   225                                                                 
T 270    K   226                                                                 
G 271    G   227                                                                 
A 272    N   228                                                                 
L 273    Y   229                                                                 
I 274    F   230                                                                 
Y 275    Y   231                                                                 
N 276    N   232                                                                 
Y 277    L   233                                                                 
G 278    S   234                                                                 
Q 279    R   236                                                                 
L 280    M   237                                                                 
Q 281    P   238                                                                 
Q 282    K   239                                                                 
I 283    V   240                                                                 
G 284    Q   241                                                                 
G 285    G   242                                                                 
T 286    N   243                                                                 
S 287    T   244                                                                 
L 288    L   245                                                                 
A 289    L   246                                                                 
S 290    N   250                                                                 
P 291    N   251                                                                 
I 292    L   252                                                                 
F 293    F   253                                                                 
V 294    H   254                                                                 
G 295    N   255                                                                 
L 296    F   256                                                                 
W 297    D   257                                                                 
A 298    G   258                                                                 
R 299    H   259                                                                 
L 300    A   260                                                                 
Q 301    F   261                                                                 
S 302    E   262                                                                 
A 303    I   263                                                                 
N 304    G   264                                                                 
S 305    T   265                                                                 
N 306    G   266                                                                 
S 307    G   267                                                                 
L 308    Y   268                                                                 
G 309    V   269                                                                 
F 310    L   270                                                                 
P 311    A   271                                                                 
A 312    E   272                                                                 
A 313    G   273                                                                 
S 314    N   274                                                                 
F 315    V   275                                                                 
Y 316    F   276                                                                 
S 317    Q   277                                                                 
A 318    D   278                                                                 
I 319    V   279                                                                 
H 327    N   280                                                                 
D 328    V   281                                                                 
V 329    V   282                                                                 
K 330    V   283                                                                 
S 331    E   284                                                                 
G 332    T   285                                                                 
G 335    P   286                                                                 
Y 336    I   287                                                                 
G 337    S   288                                                                 
G 338    G   289                                                                 
Y 339    Q   290                                                                 
G 340    L   291                                                                 
Y 341    F   292                                                                 
N 342    S   293                                                                 
A 343    S   294                                                                 
G 344    P   295                                                                 
S 355    D   296                                                                 
L 356    A   297                                                                 
D 357    N   298                                                                 
I 358    T   299                                                                 
A 359    N   300                                                                 
K 360    Q   301                                                                 
L 361    Q   302                                                                 
S 362    C   303                                                                 
A 363    A   304                                                                 
N 368    S   305                                                                 
G 369    V   306                                                                 
F 370    F   307                                                                 
G 371    G   308                                                                 
H 372    R   309                                                                 
TER                                                                              
END                                                                              



