
PFRMAT AL                                                                        
TARGET T0105                                                                     
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  1                                                                         
PARENT 1ITB_B                                                                    
D 595    A    19                                                                 
E 596    N    20                                                                 
N 597    E    21                                                                 
I 598    I    22                                                                 
N 599    D    23                                                                 
F 600    V    24                                                                 
K 601    R    25                                                                 
Q 602    P    26                                                                 
S 603    C    27                                                                 
E 604    P    28                                                                 
L 605    L    29                                                                 
T 608    N    30                                                                 
C 609    P    31                                                                 
G 610    N    32                                                                 
E 611    E    33                                                                 
V 612    H    34                                                                 
K 613    K    35                                                                 
G 614    G    36                                                                 
T 615    T    39                                                                 
L 616    W    40                                                                 
Y 617    Y    41                                                                 
K 618    K    42                                                                 
E 619    D    43                                                                 
R 620    D    44                                                                 
F 621    S    45                                                                 
K 622    K    46                                                                 
Q 623    T    47                                                                 
G 624    P    48                                                                 
T 625    V    49                                                                 
S 626    A    54                                                                 
K 627    S    55                                                                 
K 628    R    56                                                                 
C 629    I    57                                                                 
I 630    H    58                                                                 
Q 631    Q    59                                                                 
S 632    H    60                                                                 
E 633    K    61                                                                 
D 634    E    62                                                                 
K 635    K    63                                                                 
K 636    L    64                                                                 
W 637    W    65                                                                 
F 638    F    66                                                                 
T 639    V    67                                                                 
P 640    P    68                                                                 
R 641    A    69                                                                 
E 642    K    70                                                                 
F 643    V    71                                                                 
E 644    E    72                                                                 
I 645    D    73                                                                 
E 646    S    74                                                                 
G 647    G    75                                                                 
N 654    H    76                                                                 
W 655    Y    77                                                                 
K 656    Y    78                                                                 
L 657    C    79                                                                 
S 658    V    80                                                                 
I 659    V    81                                                                 
R 660    R    82                                                                 
C 661    N    83                                                                 
G 662    S    84                                                                 
G 663    S    85                                                                 
Y 664    Y    86                                                                 
T 665    C    87                                                                 
L 666    L    88                                                                 
K 667    R    89                                                                 
V 668    I    90                                                                 
L 669    K    91                                                                 
M 670    I    92                                                                 
E 671    S    93                                                                 
N 672    A    94                                                                 
K 673    K    95                                                                 
F 674    F    96                                                                 
L 675    V    97                                                                 
P 676    E    98                                                                 
E 677    N    99                                                                 
P 678    E   100                                                                 
P 679    P   101                                                                 
TER                                                                              
END                                                                              



