
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  3                                                                         
PARENT 256B_A                                                                    
G 123    A     1                                                                 
C 124    D     2                                                                 
L 125    L     3                                                                 
P 126    E     4                                                                 
A 127    D     5                                                                 
Y 128    N     6                                                                 
D 129    M     7                                                                 
A 130    E     8                                                                 
L 131    T     9                                                                 
A 132    L    10                                                                 
G 133    L    14                                                                 
Q 134    K    15                                                                 
F 135    V    16                                                                 
I 136    I    17                                                                 
E 137    E    18                                                                 
A 138    K    19                                                                 
S 139    A    20                                                                 
S 140    D    21                                                                 
R 141    T    31                                                                 
E 142    K    32                                                                 
A 143    M    33                                                                 
R 144    R    34                                                                 
Q 145    A    35                                                                 
A 146    A    36                                                                 
I 147    A    37                                                                 
L 148    L    38                                                                 
K 149    D    39                                                                 
Q 150    A    40                                                                 
G 151    Q    41                                                                 
Q 152    K    42                                                                 
D 153    A    43                                                                 
G 154    K    47                                                                 
L 155    L    48                                                                 
S 156    E    49                                                                 
G 157    D    50                                                                 
V 158    K    51                                                                 
K 159    S    52                                                                 
E 160    P    53                                                                 
T 161    D    54                                                                 
D 162    S    55                                                                 
K 163    P    56                                                                 
K 164    E    57                                                                 
W 165    M    58                                                                 
S 167    K    59                                                                 
Q 168    D    60                                                                 
Y 169    F    61                                                                 
L 170    R    62                                                                 
K 171    H    63                                                                 
I 172    G    64                                                                 
M 173    F    65                                                                 
G 174    D    66                                                                 
K 175    I    67                                                                 
I 176    L    68                                                                 
L 177    V    69                                                                 
D 178    G    70                                                                 
Q 179    Q    71                                                                 
L 188    I    72                                                                 
A 189    D    73                                                                 
R 190    D    74                                                                 
I 191    A    75                                                                 
S 192    L    76                                                                 
K 193    K    77                                                                 
L 194    L    78                                                                 
I 195    A    79                                                                 
E 196    N    80                                                                 
N 197    E    81                                                                 
K 198    G    82                                                                 
K 203    K    83                                                                 
K 204    V    84                                                                 
E 205    K    85                                                                 
E 206    E    86                                                                 
L 207    A    87                                                                 
Q 208    Q    88                                                                 
R 209    A    89                                                                 
S 210    A    90                                                                 
L 211    A    91                                                                 
N 212    E    92                                                                 
I 213    Q    93                                                                 
L 214    L    94                                                                 
T 215    K    95                                                                 
A 216    T    96                                                                 
F 217    T    97                                                                 
R 218    R    98                                                                 
K 219    N    99                                                                 
A 222    A   100                                                                 
E 223    Y   101                                                                 
K 224    H   102                                                                 
E 225    Q   103                                                                 
E 226    K   104                                                                 
L 227    Y   105                                                                 
TER                                                                              
END                                                                              



