
PFRMAT AL                                                                        
TARGET T0109                                                                     
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 1TAU_A                                                                    
M   1    L   574                                                                 
S   2    S   575                                                                 
F   3    S   576                                                                 
D   4    S   577                                                                 
K   5    D   578                                                                 
Q   6    P   579                                                                 
N   7    N   580                                                                 
L   8    L   581                                                                 
I   9    Q   582                                                                 
W  10    R   587                                                                 
I  11    T   588                                                                 
D  12    P   589                                                                 
L  13    L   590                                                                 
E  14    I   594                                                                 
M  15    R   595                                                                 
T  16    R   596                                                                 
G  17    G   597                                                                 
L  18    F   598                                                                 
D  19    I   599                                                                 
P  20    A   600                                                                 
E  21    E   601                                                                 
K  22    E   602                                                                 
E  23    G   603                                                                 
R  24    W   604                                                                 
I  25    L   605                                                                 
I  26    L   606                                                                 
E  27    V   607                                                                 
I  28    A   608                                                                 
T  30    L   609                                                                 
I  31    D   610                                                                 
V  32    Y   611                                                                 
T  33    S   612                                                                 
D  34    Q   613                                                                 
K  35    I   614                                                                 
N  36    E   615                                                                 
L  37    L   616                                                                 
N  38    R   617                                                                 
I  39    V   618                                                                 
L  40    L   619                                                                 
A  41    A   620                                                                 
E  42    H   621                                                                 
G  43    E   626                                                                 
P  44    N   627                                                                 
V  45    L   628                                                                 
L  46    I   629                                                                 
A  47    R   630                                                                 
V  48    V   631                                                                 
H  49    F   632                                                                 
Q  50    E   634                                                                 
S  51    G   635                                                                 
D  52    R   636                                                                 
E  53    D   637                                                                 
L  54    I   638                                                                 
L  55    H   639                                                                 
N  56    T   640                                                                 
K  57    E   641                                                                 
M  58    T   642                                                                 
N  59    A   643                                                                 
D  60    S   644                                                                 
W  61    W   645                                                                 
C  62    M   646                                                                 
Q  63    F   647                                                                 
K  64    G   648                                                                 
T  65    V   649                                                                 
H  66    P   650                                                                 
S  67    R   651                                                                 
I  75    E   652                                                                 
K  76    A   653                                                                 
A  77    V   654                                                                 
S  78    D   655                                                                 
K  79    P   656                                                                 
L  80    L   657                                                                 
T  81    M   658                                                                 
E  82    R   659                                                                 
R  83    R   660                                                                 
A  84    A   661                                                                 
A  85    A   662                                                                 
E  86    K   663                                                                 
T  89    T   664                                                                 
L  90    I   665                                                                 
D  91    N   666                                                                 
F  92    F   667                                                                 
L  93    G   668                                                                 
K  94    V   669                                                                 
K  95    L   670                                                                 
W  96    Y   671                                                                 
P 103    G   672                                                                 
I 104    M   673                                                                 
C 105    S   674                                                                 
G 106    A   675                                                                 
N 107    H   676                                                                 
S 108    R   677                                                                 
I 109    L   678                                                                 
A 110    S   679                                                                 
Q 111    Q   680                                                                 
D 112    E   681                                                                 
K 113    Q   690                                                                 
R 114    A   691                                                                 
F 115    F   692                                                                 
L 116    I   693                                                                 
V 117    E   694                                                                 
K 118    R   695                                                                 
Y 119    Y   696                                                                 
M 120    F   697                                                                 
P 121    Q   698                                                                 
D 122    S   699                                                                 
Y 126    F   700                                                                 
F 127    P   701                                                                 
H 128    K   702                                                                 
Y 129    V   703                                                                 
R 130    R   704                                                                 
H 131    A   705                                                                 
L 132    W   706                                                                 
D 133    I   707                                                                 
V 134    E   708                                                                 
S 135    K   709                                                                 
T 136    T   710                                                                 
L 137    L   711                                                                 
K 138    E   712                                                                 
E 139    E   713                                                                 
L 140    G   714                                                                 
R 143    R   715                                                                 
W 144    R   716                                                                 
K 145    R   717                                                                 
P 146    G   718                                                                 
E 147    Y   719                                                                 
I 148    V   720                                                                 
L 149    E   721                                                                 
E 150    T   722                                                                 
G 151    L   723                                                                 
F 152    F   724                                                                 
K 153    G   725                                                                 
K 154    R   726                                                                 
E 155    R   727                                                                 
N 156    R   728                                                                 
T 157    Y   729                                                                 
H 158    V   730                                                                 
L 159    P   731                                                                 
A 160    D   732                                                                 
L 161    L   733                                                                 
D 162    K   738                                                                 
D 163    S   739                                                                 
I 164    V   740                                                                 
R 165    R   741                                                                 
E 166    E   742                                                                 
S 167    A   743                                                                 
I 168    A   744                                                                 
K 169    E   745                                                                 
E 170    R   746                                                                 
L 171    M   747                                                                 
A 172    A   748                                                                 
Y 173    F   749                                                                 
Y 174    N   750                                                                 
R 175    M   751                                                                 
E 176    A   758                                                                 
H 177    D   759                                                                 
F 178    L   760                                                                 
M 179    M   761                                                                 
K 180    K   762                                                                 
L 181    L   763                                                                 
D 182    A   764                                                                 
TER                                                                              
END                                                                              



