
PFRMAT AL                                                                        
TARGET T0097                                                                     
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  1                                                                         
PARENT 1QSD_A                                                                    
G 123    T     4                                                                 
C 124    Q     5                                                                 
Y 128    L     6                                                                 
D 129    D     7                                                                 
A 130    I     8                                                                 
L 131    K     9                                                                 
A 132    V    10                                                                 
G 133    K    11                                                                 
Q 134    A    12                                                                 
F 135    L    13                                                                 
I 136    K    14                                                                 
E 137    R    15                                                                 
A 138    L    16                                                                 
S 139    T    17                                                                 
S 140    K    18                                                                 
R 141    E    19                                                                 
E 142    E    20                                                                 
A 143    Y    22                                                                 
R 144    Y    23                                                                 
Q 145    Q    24                                                                 
A 146    Q    25                                                                 
I 147    E    26                                                                 
L 148    L    27                                                                 
K 149    K    28                                                                 
Q 150    D    29                                                                 
G 151    Q    30                                                                 
Q 152    E    31                                                                 
D 153    A    32                                                                 
G 154    H    33                                                                 
L 155    V    34                                                                 
S 156    A    35                                                                 
G 157    K    36                                                                 
V 158    L    37                                                                 
K 159    K    38                                                                 
E 160    E    39                                                                 
K 163    D    40                                                                 
K 164    K    41                                                                 
W 165    S    42                                                                 
A 166    V    43                                                                 
S 167    D    44                                                                 
Q 168    P    45                                                                 
Y 169    D    47                                                                 
L 170    L    48                                                                 
K 171    K    49                                                                 
I 172    K    50                                                                 
M 173    Q    51                                                                 
G 174    E    52                                                                 
K 175    E    53                                                                 
I 176    V    54                                                                 
L 177    L    55                                                                 
D 178    D    56                                                                 
Q 179    D    57                                                                 
L 188    T    58                                                                 
A 189    K    59                                                                 
R 190    R    60                                                                 
I 191    L    61                                                                 
S 192    L    62                                                                 
K 193    P    63                                                                 
L 194    T    64                                                                 
I 195    L    65                                                                 
E 196    Y    66                                                                 
N 197    E    67                                                                 
K 198    K    68                                                                 
M 199    I    69                                                                 
S 200    R    70                                                                 
E 201    E    71                                                                 
G 202    F    72                                                                 
K 204    K    73                                                                 
E 205    E    74                                                                 
E 206    D    75                                                                 
L 207    L    76                                                                 
Q 208    E    77                                                                 
R 209    Q    78                                                                 
S 210    F    79                                                                 
L 211    L    80                                                                 
N 212    E    87                                                                 
I 213    D    88                                                                 
L 214    V    89                                                                 
T 215    S    90                                                                 
A 216    D    91                                                                 
F 217    A    92                                                                 
R 218    R    93                                                                 
K 219    S    94                                                                 
K 220    A    95                                                                 
G 221    I    96                                                                 
A 222    T    97                                                                 
E 223    S    98                                                                 
K 224    A    99                                                                 
E 225    Q   100                                                                 
E 226    E   101                                                                 
L 227    L   102                                                                 
TER                                                                              
END                                                                              



