
PFRMAT AL                                                                        
TARGET T0121                                                                     
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 1B9N_B                                                                    
I 251    Q   145                                                                 
T 253    H   146                                                                 
E 254    V   147                                                                 
D 255    D   148                                                                 
G 256    V   149                                                                 
F 257    L   150                                                                 
V 258    L   151                                                                 
D 259    A   152                                                                 
F 260    D   153                                                                 
G 261    G   154                                                                 
E 262    K   155                                                                 
F 263    T   156                                                                 
R 264    R   157                                                                 
L 265    L   158                                                                 
K 266    K   159                                                                 
L 267    V   160                                                                 
L 268    I   162                                                                 
P 269    T   163                                                                 
D 270    A   164                                                                 
Q 271    Q   165                                                                 
F 272    S   166                                                                 
E 273    G   167                                                                 
V 274    A   168                                                                 
L 275    R   169                                                                 
G 276    L   170                                                                 
E 277    G   171                                                                 
L 278    L   172                                                                 
G 279    D   173                                                                 
V 281    E   174                                                                 
G 282    G   175                                                                 
R 283    K   176                                                                 
E 284    E   177                                                                 
V 285    V   178                                                                 
I 286    L   179                                                                 
F 287    I   180                                                                 
G 288    L   181                                                                 
I 289    L   182                                                                 
R 290    K   183                                                                 
P 291    A   184                                                                 
E 292    P   185                                                                 
D 293    W   186                                                                 
L 294    V   187                                                                 
Y 295    G   188                                                                 
D 296    I   189                                                                 
A 297    T   190                                                                 
M 298    Q   191                                                                 
F 299    D   192                                                                 
A 300    E   193                                                                 
R 301    A   194                                                                 
V 302    V   195                                                                 
R 303    A   196                                                                 
V 304    Q   197                                                                 
P 305    N   198                                                                 
G 306    A   199                                                                 
E 307    D   200                                                                 
N 308    N   201                                                                 
L 309    Q   202                                                                 
V 310    L   203                                                                 
R 311    P   204                                                                 
A 312    G   205                                                                 
V 313    I   206                                                                 
V 314    I   207                                                                 
E 315    S   208                                                                 
I 316    H   209                                                                 
V 317    I   210                                                                 
E 318    E   211                                                                 
N 319    R   212                                                                 
L 320    G   213                                                                 
G 321    A   214                                                                 
S 322    E   215                                                                 
E 323    Q   216                                                                 
R 324    C   217                                                                 
I 325    E   218                                                                 
V 326    V   219                                                                 
H 327    L   220                                                                 
L 328    M   221                                                                 
R 329    A   222                                                                 
V 330    L   223                                                                 
G 331    D   225                                                                 
G 332    G   226                                                                 
V 333    Q   227                                                                 
T 334    T   228                                                                 
F 335    L   229                                                                 
V 336    C   230                                                                 
G 337    A   231                                                                 
A 338    T   232                                                                 
F 339    V   235                                                                 
R 340    N   236                                                                 
S 341    E   237                                                                 
E 342    A   238                                                                 
S 343    T   239                                                                 
R 344    S   240                                                                 
V 345    L   241                                                                 
R 346    Q   242                                                                 
E 347    Q   243                                                                 
G 348    G   244                                                                 
V 349    Q   245                                                                 
E 350    N   246                                                                 
V 351    V   247                                                                 
D 352    T   248                                                                 
V 353    A   249                                                                 
V 354    Y   250                                                                 
F 355    F   251                                                                 
D 356    N   252                                                                 
M 357    A   253                                                                 
K 358    D   254                                                                 
K 359    S   255                                                                 
I 360    V   256                                                                 
H 361    I   257                                                                 
I 362    I   258                                                                 
K 369    A   259                                                                 
A 370    T   260                                                                 
I 371    L   261                                                                 
F 372    C   262                                                                 
TER                                                                              
END                                                                              



