
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  3                                                                         
PARENT 3PCY                                                                      
D 595    D     9                                                                 
E 596    G    10                                                                 
N 597    S    11                                                                 
I 598    L    12                                                                 
N 599    A    13                                                                 
F 600    F    14                                                                 
K 601    V    15                                                                 
Q 602    P    16                                                                 
S 603    S    17                                                                 
E 604    E    18                                                                 
L 605    F    19                                                                 
P 606    S    20                                                                 
V 607    I    21                                                                 
T 608    S    22                                                                 
C 609    P    23                                                                 
G 610    G    24                                                                 
E 611    E    25                                                                 
V 612    K    26                                                                 
K 613    I    27                                                                 
G 614    N    38                                                                 
T 615    I    39                                                                 
L 616    V    40                                                                 
Y 617    F    41                                                                 
K 618    D    42                                                                 
E 619    E    43                                                                 
R 620    D    44                                                                 
F 621    I    46                                                                 
K 622    P    47                                                                 
Q 623    S    48                                                                 
G 624    G    49                                                                 
T 625    V    50                                                                 
S 626    D    51                                                                 
K 627    A    52                                                                 
K 628    S    53                                                                 
C 629    K    54                                                                 
I 630    I    55                                                                 
Q 631    S    56                                                                 
S 632    M    57                                                                 
E 633    S    58                                                                 
D 634    E    59                                                                 
K 635    E    60                                                                 
K 636    D    61                                                                 
W 637    L    62                                                                 
F 638    L    63                                                                 
R 660    N    64                                                                 
C 661    A    65                                                                 
G 662    K    66                                                                 
G 663    G    67                                                                 
Y 664    E    68                                                                 
T 665    T    69                                                                 
L 666    F    70                                                                 
K 667    E    71                                                                 
V 668    V    72                                                                 
L 669    A    73                                                                 
M 670    L    74                                                                 
E 671    S    75                                                                 
N 672    N    76                                                                 
K 673    S    81                                                                 
F 674    F    82                                                                 
L 675    Y    83                                                                 
P 676    C    84                                                                 
E 677    S    85                                                                 
P 678    P    86                                                                 
P 679    A    90                                                                 
S 680    G    91                                                                 
T 681    M    92                                                                 
R 682    V    93                                                                 
K 683    G    94                                                                 
K 684    K    95                                                                 
V 685    V    96                                                                 
T 686    T    97                                                                 
I 687    V    98                                                                 
K 688    N    99                                                                 
TER                                                                              
END                                                                              



