
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  4                                                                         
PARENT 1GRJ                                                                      
D 595    N    83                                                                 
E 596    G    84                                                                 
N 597    R    85                                                                 
I 598    V    86                                                                 
N 599    I    87                                                                 
F 600    F    88                                                                 
K 601    G    89                                                                 
L 605    A    90                                                                 
P 606    T    91                                                                 
V 607    V    92                                                                 
T 608    T    93                                                                 
C 609    V    94                                                                 
G 610    L    95                                                                 
E 611    N    96                                                                 
I 630    L    97                                                                 
Q 631    D    98                                                                 
S 632    S    99                                                                 
E 633    D   100                                                                 
D 634    E   101                                                                 
K 635    E   102                                                                 
K 636    Q   103                                                                 
E 642    T   104                                                                 
F 643    Y   105                                                                 
E 644    R   106                                                                 
I 645    I   107                                                                 
E 646    V   108                                                                 
G 647    G   109                                                                 
D 648    D   110                                                                 
R 649    D   111                                                                 
G 650    E   112                                                                 
A 651    A   113                                                                 
S 652    D   114                                                                 
K 653    F   115                                                                 
N 654    K   116                                                                 
W 655    Q   117                                                                 
L 657    N   118                                                                 
S 658    L   119                                                                 
I 659    I   120                                                                 
R 660    S   121                                                                 
C 661    V   122                                                                 
G 662    N   123                                                                 
G 663    S   124                                                                 
Y 664    P   125                                                                 
T 665    I   126                                                                 
L 666    A   127                                                                 
K 667    R   128                                                                 
V 668    G   129                                                                 
L 669    L   130                                                                 
M 670    I   131                                                                 
E 671    G   132                                                                 
N 672    D   137                                                                 
K 673    V   138                                                                 
F 674    V   139                                                                 
L 675    V   140                                                                 
P 676    I   141                                                                 
K 683    V   148                                                                 
K 684    E   149                                                                 
V 685    F   150                                                                 
T 686    E   151                                                                 
I 687    V   152                                                                 
K 688    I   153                                                                 
TER                                                                              
END                                                                              



