
PFRMAT AL                                                                        
TARGET T0110                                                                     
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 7REQ_A                                                                    
M   1    V   569                                                                 
A   2    S   571                                                                 
R   3    K   572                                                                 
E   4    E   573                                                                 
F   5    V   574                                                                 
K   6    K   575                                                                 
R   7    N   576                                                                 
S   8    T   577                                                                 
D   9    P   578                                                                 
V  11    E   579                                                                 
A  12    V   580                                                                 
Q  13    E   581                                                                 
E  14    E   582                                                                 
I  15    A   583                                                                 
Q  16    R   584                                                                 
K  17    E   585                                                                 
E  18    L   586                                                                 
I  19    V   587                                                                 
A  20    E   588                                                                 
V  21    E   589                                                                 
I  22    F   590                                                                 
L  23    E   591                                                                 
Q  24    Q   592                                                                 
R  25    A   593                                                                 
E  26    E   594                                                                 
V  27    G   595                                                                 
K  28    R   596                                                                 
D  29    R   597                                                                 
P  30    P   598                                                                 
R  31    R   599                                                                 
I  32    I   600                                                                 
G  33    L   601                                                                 
M  34    L   602                                                                 
V  35    A   603                                                                 
T  36    K   604                                                                 
V  37    M   605                                                                 
S  38    G   606                                                                 
D  39    Q   607                                                                 
V  40    D   608                                                                 
E  41    G   609                                                                 
V  42    H   610                                                                 
S  43    D   611                                                                 
S  44    R   612                                                                 
D  45    A   618                                                                 
L  46    T   619                                                                 
S  47    A   620                                                                 
Y  48    Y   621                                                                 
A  49    A   622                                                                 
K  50    D   627                                                                 
I  51    V   628                                                                 
F  52    D   629                                                                 
V  53    V   630                                                                 
T  54    G   631                                                                 
F  55    P   632                                                                 
L  56    L   633                                                                 
F  57    F   634                                                                 
D  58    Q   635                                                                 
H  59    T   636                                                                 
D  60    P   637                                                                 
E  61    E   638                                                                 
M  62    E   639                                                                 
A  63    T   640                                                                 
I  64    A   641                                                                 
E  65    R   642                                                                 
Q  66    Q   643                                                                 
G  70    A   644                                                                 
L  71    V   645                                                                 
E  72    E   646                                                                 
K  73    A   647                                                                 
A  74    D   648                                                                 
S  75    V   649                                                                 
P  76    H   650                                                                 
Y  77    V   651                                                                 
I  78    V   652                                                                 
R  79    G   653                                                                 
S  80    V   654                                                                 
L  81    S   655                                                                 
L  82    S   656                                                                 
G  83    L   657                                                                 
K  84    A   658                                                                 
A  85    G   659                                                                 
M  86    G   660                                                                 
R  87    H   661                                                                 
L  88    L   662                                                                 
R  89    T   663                                                                 
I  90    L   664                                                                 
V  91    V   665                                                                 
P  92    P   666                                                                 
E  93    A   667                                                                 
I  94    L   668                                                                 
R  95    R   669                                                                 
F  96    K   670                                                                 
I  97    E   671                                                                 
L 102    L   672                                                                 
V 103    D   673                                                                 
E 104    K   674                                                                 
G 105    L   675                                                                 
M 106    G   676                                                                 
R 107    R   677                                                                 
M 108    P   678                                                                 
S 109    D   679                                                                 
N 110    I   680                                                                 
L 111    L   681                                                                 
V 112    I   682                                                                 
T 113    G   685                                                                 
N 114    G   686                                                                 
V 115    V   687                                                                 
V 116    I   688                                                                 
R 117    P   689                                                                 
E 118    E   690                                                                 
D 119    Q   691                                                                 
E 120    D   692                                                                 
K 121    F   693                                                                 
K 122    D   694                                                                 
H 123    E   695                                                                 
V 124    L   696                                                                 
E 125    R   697                                                                 
E 126    K   698                                                                 
S 127    D   699                                                                 
N 128    G   700                                                                 
TER                                                                              
END                                                                              



