
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  2                                                                         
PARENT 1EUT                                                                      
D 595    G   403                                                                 
E 596    I   404                                                                 
N 597    C   405                                                                 
I 598    A   406                                                                 
N 599    P   407                                                                 
F 600    F   408                                                                 
K 601    T   409                                                                 
Q 602    I   410                                                                 
S 603    P   411                                                                 
E 604    D   412                                                                 
L 605    V   413                                                                 
P 606    A   414                                                                 
V 607    L   415                                                                 
T 608    E   416                                                                 
C 609    P   417                                                                 
G 610    G   418                                                                 
E 611    Q   419                                                                 
V 612    V   423                                                                 
K 613    P   424                                                                 
G 614    V   425                                                                 
T 615    A   426                                                                 
L 616    V   427                                                                 
Y 617    T   428                                                                 
S 632    N   429                                                                 
E 633    Q   430                                                                 
D 634    S   431                                                                 
K 635    G   432                                                                 
K 636    I   433                                                                 
W 637    A   434                                                                 
F 638    V   435                                                                 
T 639    P   436                                                                 
P 640    K   437                                                                 
R 641    P   438                                                                 
E 642    S   439                                                                 
F 643    L   440                                                                 
E 644    Q   441                                                                 
I 645    L   442                                                                 
E 646    D   443                                                                 
G 647    A   444                                                                 
S 652    S   445                                                                 
K 653    P   446                                                                 
N 654    D   447                                                                 
W 655    W   448                                                                 
K 656    Q   449                                                                 
L 657    V   450                                                                 
S 658    Q   451                                                                 
I 659    G   452                                                                 
R 660    S   453                                                                 
C 661    V   454                                                                 
G 662    E   455                                                                 
G 663    P   456                                                                 
Y 664    L   457                                                                 
T 665    Q   462                                                                 
L 666    A   463                                                                 
K 667    K   464                                                                 
V 668    G   465                                                                 
L 669    Q   466                                                                 
M 670    V   467                                                                 
E 671    T   468                                                                 
N 672    I   469                                                                 
K 673    T   470                                                                 
F 674    V   471                                                                 
L 675    P   472                                                                 
P 676    A   473                                                                 
E 677    G   474                                                                 
P 678    T   475                                                                 
P 679    T   476                                                                 
S 680    P   477                                                                 
T 681    G   478                                                                 
R 682    R   479                                                                 
K 683    Y   480                                                                 
K 684    R   481                                                                 
V 685    V   482                                                                 
T 686    G   483                                                                 
I 687    A   484                                                                 
K 688    T   485                                                                 
TER                                                                              
END                                                                              



