
PFRMAT AL                                                                        
TARGET T0104                                                                     
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 1QF7_B                                                                    
M   1    V   598                                                                 
E   2    K   599                                                                 
S   3    G   600                                                                 
L   4    V   603                                                                 
T   5    A   604                                                                 
Q   6    I   605                                                                 
Y   7    L   606                                                                 
I   8    L   607                                                                 
P   9    N   608                                                                 
D  10    D   609                                                                 
E  11    E   610                                                                 
F  12    V   611                                                                 
S  13    R   612                                                                 
M  14    S   613                                                                 
K  19    A   614                                                                 
K  20    D   615                                                                 
F  21    L   616                                                                 
A  22    L   617                                                                 
E  23    A   618                                                                 
I  24    I   619                                                                 
L  25    L   620                                                                 
L  26    K   621                                                                 
K  27    A   622                                                                 
L  28    L   623                                                                 
H  29    K   624                                                                 
T  30    A   625                                                                 
E  31    K   626                                                                 
K  32    G   627                                                                 
A  33    V   628                                                                 
I  34    H   629                                                                 
M  35    A   630                                                                 
V  36    K   631                                                                 
Y  37    L   632                                                                 
L  38    L   633                                                                 
N  39    Y   634                                                                 
G  40    S   635                                                                 
D  41    R   636                                                                 
L  42    M   637                                                                 
G  43    G   638                                                                 
A  44    E   639                                                                 
G  45    V   640                                                                 
K  46    T   641                                                                 
G  58    A   642                                                                 
H  59    D   643                                                                 
Q  60    D   644                                                                 
G  61    G   645                                                                 
N  62    T   646                                                                 
V  63    V   647                                                                 
K  64    L   648                                                                 
S  65    P   649                                                                 
P  66    I   650                                                                 
T  67    A   651                                                                 
Y  68    A   652                                                                 
T  69    T   653                                                                 
L  70    F   654                                                                 
V  71    A   655                                                                 
E  72    G   656                                                                 
E  73    A   657                                                                 
Y  74    P   658                                                                 
N  75    S   659                                                                 
I  76    L   660                                                                 
A  77    T   661                                                                 
G  78    V   662                                                                 
K  79    D   663                                                                 
M  80    A   664                                                                 
I  81    V   665                                                                 
Y  82    I   666                                                                 
H  83    C   669                                                                 
F  84    G   670                                                                 
D  85    N   671                                                                 
L  86    I   672                                                                 
Y  87    A   673                                                                 
R  88    D   674                                                                 
L  89    I   675                                                                 
A  90    A   676                                                                 
D  91    D   677                                                                 
P  92    N   678                                                                 
E  93    G   679                                                                 
E  94    D   680                                                                 
L  95    A   681                                                                 
E  96    N   682                                                                 
F  97    Y   683                                                                 
M  98    Y   684                                                                 
G  99    L   685                                                                 
I 100    M   686                                                                 
R 101    E   687                                                                 
D 102    A   688                                                                 
Y 103    Y   689                                                                 
F 104    K   690                                                                 
N 105    H   691                                                                 
T 106    L   692                                                                 
D 107    K   693                                                                 
S 108    P   694                                                                 
I 109    I   695                                                                 
C 110    A   696                                                                 
L 111    L   697                                                                 
I 112    A   698                                                                 
E 113    G   699                                                                 
W 114    D   700                                                                 
S 115    A   701                                                                 
E 116    R   702                                                                 
K 117    K   703                                                                 
G 118    F   704                                                                 
Q 119    K   705                                                                 
G 120    I   710                                                                 
I 121    A   711                                                                 
L 122    D   712                                                                 
P 123    Q   713                                                                 
E 124    G   714                                                                 
A 125    E   715                                                                 
D 126    E   716                                                                 
I 127    G   717                                                                 
L 128    I   718                                                                 
V 129    V   719                                                                 
N 130    E   720                                                                 
I 131    A   721                                                                 
D 132    D   722                                                                 
Y 133    S   723                                                                 
Y 134    A   724                                                                 
D 135    D   725                                                                 
D 136    G   726                                                                 
A 137    S   727                                                                 
R 138    F   728                                                                 
N 139    M   729                                                                 
I 140    D   730                                                                 
E 141    E   731                                                                 
L 142    L   732                                                                 
I 143    L   733                                                                 
A 144    T   734                                                                 
Q 145    L   735                                                                 
T 146    M   736                                                                 
N 147    H   739                                                                 
L 148    R   740                                                                 
G 149    V   741                                                                 
K 150    W   742                                                                 
N 151    S   743                                                                 
I 152    R   744                                                                 
I 153    I   745                                                                 
S 154    P   746                                                                 
A 155    K   747                                                                 
F 156    I   751                                                                 
S 157    P   752                                                                 
N 158    A   753                                                                 
TER                                                                              
END                                                                              



