
PFRMAT AL                                                                        
TARGET T0101                                                                     
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 1KAP_P                                                                    
T  96    G   247                                                                 
F  97    A   248                                                                 
N  98    N   249                                                                 
K  99    L   250                                                                 
S 100    T   251                                                                 
G 101    T   252                                                                 
K 102    R   253                                                                 
D 103    T   254                                                                 
G 104    G   255                                                                 
A 105    D   256                                                                 
P 106    T   257                                                                 
I 107    V   258                                                                 
Y 108    Y   259                                                                 
V 109    G   260                                                                 
A 110    F   261                                                                 
A 111    N   262                                                                 
A 112    S   263                                                                 
N 113    N   264                                                                 
C 114    T   265                                                                 
G 115    E   266                                                                 
R 116    R   267                                                                 
A 117    D   268                                                                 
V 118    F   269                                                                 
F 119    Y   270                                                                 
D 120    S   271                                                                 
F 121    A   272                                                                 
S 122    T   273                                                                 
F 123    S   274                                                                 
P 124    S   275                                                                 
D 125    S   276                                                                 
S 126    S   277                                                                 
S 132    K   278                                                                 
Y 133    L   279                                                                 
G 134    V   280                                                                 
F 135    F   281                                                                 
Y 136    S   282                                                                 
V 137    V   283                                                                 
Y 158    W   284                                                                 
V 159    D   285                                                                 
I 160    A   286                                                                 
G 161    G   287                                                                 
S 162    G   288                                                                 
H 163    N   289                                                                 
N 164    D   290                                                                 
T 165    T   291                                                                 
F 166    L   292                                                                 
E 167    D   293                                                                 
N 168    F   294                                                                 
T 169    S   295                                                                 
A 170    G   296                                                                 
F 171    F   297                                                                 
H 172    S   298                                                                 
H 173    Q   299                                                                 
N 174    N   300                                                                 
R 175    Q   301                                                                 
N 176    K   302                                                                 
T 177    I   303                                                                 
G 178    N   319                                                                 
L 179    V   320                                                                 
E 180    S   321                                                                 
I 181    I   322                                                                 
N 182    A   323                                                                 
N 183    A   324                                                                 
G 184    G   325                                                                 
G 185    V   326                                                                 
S 186    T   327                                                                 
Y 187    V   328                                                                 
N 188    E   329                                                                 
T 189    N   330                                                                 
V 190    A   331                                                                 
I 191    I   332                                                                 
N 192    G   333                                                                 
S 193    G   334                                                                 
D 194    S   335                                                                 
A 195    G   336                                                                 
Y 196    S   337                                                                 
N 204    D   338                                                                 
G 205    L   339                                                                 
S 206    L   340                                                                 
M 207    I   341                                                                 
A 208    G   342                                                                 
D 209    N   343                                                                 
G 210    D   344                                                                 
F 211    V   345                                                                 
G 212    A   346                                                                 
P 213    N   347                                                                 
K 214    V   348                                                                 
Q 215    L   349                                                                 
K 216    K   350                                                                 
Q 217    G   351                                                                 
G 218    G   352                                                                 
P 219    A   353                                                                 
G 220    G   354                                                                 
N 221    N   355                                                                 
R 222    D   356                                                                 
F 223    I   357                                                                 
V 224    L   358                                                                 
G 225    Y   359                                                                 
C 226    D   365                                                                 
R 227    Q   366                                                                 
A 228    L   367                                                                 
W 229    W   368                                                                 
E 230    G   369                                                                 
N 231    G   370                                                                 
S 232    A   371                                                                 
D 233    G   372                                                                 
D 234    A   373                                                                 
G 235    D   374                                                                 
F 236    T   375                                                                 
D 237    F   376                                                                 
L 238    V   377                                                                 
F 239    Y   378                                                                 
D 240    G   379                                                                 
S 241    D   380                                                                 
P 242    I   381                                                                 
Q 243    A   388                                                                 
K 244    P   389                                                                 
V 245    D   390                                                                 
V 246    T   391                                                                 
I 247    L   392                                                                 
E 248    R   393                                                                 
N 249    D   394                                                                 
S 250    F   395                                                                 
W 251    V   396                                                                 
A 252    S   397                                                                 
F 253    G   398                                                                 
R 254    Q   399                                                                 
N 255    D   400                                                                 
G 256    K   401                                                                 
I 257    I   402                                                                 
N 258    D   403                                                                 
Y 259    L   404                                                                 
W 260    S   405                                                                 
N 261    G   406                                                                 
D 262    L   407                                                                 
S 263    D   408                                                                 
A 264    A   409                                                                 
F 265    F   410                                                                 
A 266    V   411                                                                 
G 267    N   412                                                                 
N 268    G   413                                                                 
G 269    G   414                                                                 
N 270    L   415                                                                 
G 271    V   416                                                                 
F 272    L   417                                                                 
K 273    Q   418                                                                 
L 274    Y   419                                                                 
S 295    V   420                                                                 
K 296    D   421                                                                 
G 297    A   422                                                                 
F 298    F   423                                                                 
D 299    A   424                                                                 
Q 300    G   425                                                                 
N 301    K   426                                                                 
A 304    A   427                                                                 
G 305    G   428                                                                 
G 306    Q   429                                                                 
V 307    A   430                                                                 
T 308    I   431                                                                 
V 309    L   432                                                                 
I 310    S   433                                                                 
N 311    Y   434                                                                 
N 312    D   435                                                                 
T 313    A   436                                                                 
S 314    A   437                                                                 
Y 315    S   438                                                                 
K 316    K   439                                                                 
N 317    A   440                                                                 
G 318    G   441                                                                 
I 319    S   442                                                                 
N 320    A   444                                                                 
Y 321    I   445                                                                 
G 322    D   446                                                                 
F 323    F   447                                                                 
G 324    S   448                                                                 
S 325    G   449                                                                 
N 326    D   450                                                                 
V 327    A   451                                                                 
Q 328    H   452                                                                 
S 329    A   453                                                                 
G 330    D   454                                                                 
Q 331    F   455                                                                 
K 332    A   456                                                                 
H 333    I   457                                                                 
Y 334    N   458                                                                 
F 335    L   459                                                                 
R 336    I   460                                                                 
N 337    G   461                                                                 
N 338    Q   462                                                                 
V 339    A   463                                                                 
S 340    T   464                                                                 
L 341    Q   465                                                                 
S 342    A   466                                                                 
A 343    D   467                                                                 
S 344    I   468                                                                 
V 345    V   469                                                                 
T 346    V   470                                                                 
TER                                                                              
END                                                                              



