
PFRMAT AL                                                                        
TARGET T0095                                                                     
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 1AEP                                                                      
G 411    N     6                                                                 
N 412    I     7                                                                 
E 413    A     8                                                                 
K 414    E     9                                                                 
E 415    A    10                                                                 
V 416    V    11                                                                 
K 417    Q    12                                                                 
E 418    Q    13                                                                 
Y 419    L    14                                                                 
A 420    N    15                                                                 
Q 421    H    16                                                                 
V 422    T    17                                                                 
F 423    I    18                                                                 
R 424    V    19                                                                 
E 425    N    20                                                                 
H 426    A    21                                                                 
A 427    A    22                                                                 
N 428    H    23                                                                 
K 429    E    24                                                                 
L 430    L    25                                                                 
I 431    H    26                                                                 
E 432    E    27                                                                 
V 433    T    28                                                                 
A 434    L    29                                                                 
N 435    G    30                                                                 
I 440    L    31                                                                 
S 441    P    32                                                                 
N 442    T    33                                                                 
N 443    P    34                                                                 
E 444    D    35                                                                 
E 445    E    36                                                                 
G 446    A    37                                                                 
V 447    L    38                                                                 
K 448    N    39                                                                 
L 449    L    40                                                                 
V 450    L    41                                                                 
R 451    T    42                                                                 
M 452    E    43                                                                 
S 453    Q    44                                                                 
A 454    A    45                                                                 
S 455    N    46                                                                 
Q 456    A    47                                                                 
L 457    F    48                                                                 
E 458    K    49                                                                 
A 459    T    50                                                                 
L 460    K    51                                                                 
C 461    I    52                                                                 
P 462    A    53                                                                 
Q 463    E    54                                                                 
V 464    V    55                                                                 
I 465    T    56                                                                 
N 466    T    57                                                                 
A 467    S    58                                                                 
A 468    L    59                                                                 
L 469    K    60                                                                 
A 470    Q    61                                                                 
L 471    E    62                                                                 
A 472    A    63                                                                 
A 473    E    64                                                                 
K 474    K    65                                                                 
P 475    H    66                                                                 
Q 476    Q    67                                                                 
S 477    G    68                                                                 
K 478    S    69                                                                 
L 479    V    70                                                                 
A 480    A    71                                                                 
Q 481    E    72                                                                 
N 483    Q    73                                                                 
M 484    L    74                                                                 
D 485    N    75                                                                 
L 486    A    76                                                                 
F 487    F    77                                                                 
K 488    A    78                                                                 
E 489    R    79                                                                 
Q 490    N    80                                                                 
W 491    L    81                                                                 
E 492    N    82                                                                 
K 493    N    83                                                                 
Q 494    S    84                                                                 
V 495    I    85                                                                 
R 496    H    86                                                                 
V 497    D    87                                                                 
L 498    A    88                                                                 
T 499    A    89                                                                 
D 500    T    90                                                                 
A 501    S    91                                                                 
V 502    L    92                                                                 
D 503    N    93                                                                 
D 504    Q    97                                                                 
I 505    L    98                                                                 
T 506    N    99                                                                 
S 507    S   100                                                                 
I 508    L   101                                                                 
D 509    Q   102                                                                 
D 510    S   103                                                                 
F 511    A   104                                                                 
L 512    L   105                                                                 
A 513    T   106                                                                 
V 514    N   107                                                                 
S 515    V   108                                                                 
N 517    G   109                                                                 
H 518    H   110                                                                 
I 519    Q   111                                                                 
L 520    W   112                                                                 
E 521    Q   113                                                                 
D 522    D   114                                                                 
V 523    I   115                                                                 
N 524    A   116                                                                 
I 528    T   117                                                                 
A 529    K   118                                                                 
L 530    T   119                                                                 
Q 531    Q   120                                                                 
E 532    A   121                                                                 
K 533    S   122                                                                 
D 534    A   123                                                                 
V 535    Q   124                                                                 
D 536    E   125                                                                 
G 537    A   126                                                                 
L 538    W   127                                                                 
D 539    A   128                                                                 
R 540    P   129                                                                 
T 541    V   130                                                                 
A 542    Q   131                                                                 
G 543    S   132                                                                 
A 544    A   133                                                                 
I 545    L   134                                                                 
R 546    Q   135                                                                 
G 547    E   136                                                                 
R 548    A   137                                                                 
A 549    A   138                                                                 
A 550    E   139                                                                 
R 551    K   140                                                                 
V 552    T   141                                                                 
I 553    K   142                                                                 
H 554    E   143                                                                 
V 555    A   144                                                                 
V 556    A   145                                                                 
T 557    A   146                                                                 
S 558    N   147                                                                 
E 559    L   148                                                                 
M 560    Q   149                                                                 
D 561    N   150                                                                 
N 562    S   151                                                                 
Y 563    I   152                                                                 
E 564    Q   153                                                                 
P 565    S   154                                                                 
Y 568    A   155                                                                 
T 569    V   156                                                                 
E 570    Q   157                                                                 
K 571    K   158                                                                 
TER                                                                              
END                                                                              


                          Ralf Zimmer
  LLL    LL   LL  LLLL    German Nat.Res.Center for Information Technology
 L       L L L L  L   L   Schloss Birlinghoven, D-53754 Sankt Augustin
L  LLL   L  L  L  L    L  Tel: +49-2241-14-2818, Fax: +49-2241-14-2656
 L   L   L     L  L   L   Email: Ralf.Zimmer@gmd.de
  LLL    L     L  LLLL    WWW: http://www.gmd.de/SCAI/people/zimmer.html




