
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  2                                                                         
PARENT 2SPC_A                                                                    
G 123    Q     0                                                                 
C 124    N     1                                                                 
L 125    L     2                                                                 
P 126    Q     5                                                                 
A 127    L     6                                                                 
Y 128    Y     7                                                                 
D 129    M     8                                                                 
A 130    R     9                                                                 
L 131    D    10                                                                 
G 133    C    11                                                                 
Q 134    E    12                                                                 
F 135    L    13                                                                 
I 136    A    14                                                                 
E 137    E    15                                                                 
S 139    S    16                                                                 
S 140    W    17                                                                 
R 141    M    18                                                                 
E 142    S    19                                                                 
A 143    A    20                                                                 
R 144    R    21                                                                 
Q 145    E    22                                                                 
A 146    A    23                                                                 
I 147    F    24                                                                 
L 148    L    25                                                                 
K 149    N    26                                                                 
Q 150    A    27                                                                 
G 151    D    28                                                                 
Q 152    D    30                                                                 
D 153    A    31                                                                 
G 154    N    32                                                                 
L 155    A    33                                                                 
S 156    G    34                                                                 
G 157    G    35                                                                 
V 158    N    36                                                                 
K 159    V    37                                                                 
E 160    E    38                                                                 
T 161    A    39                                                                 
D 162    L    40                                                                 
K 163    I    41                                                                 
K 164    K    42                                                                 
W 165    K    43                                                                 
A 166    H    44                                                                 
S 167    E    45                                                                 
Q 168    D    46                                                                 
Y 169    F    47                                                                 
L 170    D    48                                                                 
K 171    K    49                                                                 
I 172    A    50                                                                 
I 176    I    51                                                                 
L 177    N    52                                                                 
D 178    G    53                                                                 
Q 179    H    54                                                                 
G 180    E    55                                                                 
E 181    Q    56                                                                 
D 182    K    57                                                                 
A 185    I    58                                                                 
S 186    A    59                                                                 
E 187    A    60                                                                 
L 188    L    61                                                                 
A 189    Q    62                                                                 
R 190    T    63                                                                 
I 191    V    64                                                                 
S 192    D    66                                                                 
K 193    Q    67                                                                 
L 194    L    68                                                                 
I 195    I    69                                                                 
E 196    A    70                                                                 
N 197    Q    71                                                                 
K 198    N    77                                                                 
M 199    L    78                                                                 
S 200    V    79                                                                 
E 201    D    80                                                                 
G 202    E    81                                                                 
K 203    K    82                                                                 
K 204    K    84                                                                 
E 205    Q    85                                                                 
E 206    V    86                                                                 
L 207    L    87                                                                 
Q 208    E    88                                                                 
R 209    R    89                                                                 
S 210    W    90                                                                 
L 211    R    91                                                                 
N 212    H    92                                                                 
I 213    L    93                                                                 
L 214    K    94                                                                 
T 215    E    95                                                                 
A 216    G    96                                                                 
F 217    L    97                                                                 
R 218    I    98                                                                 
K 219    E    99                                                                 
K 220    K   100                                                                 
G 221    R   101                                                                 
A 222    S   102                                                                 
E 223    R   103                                                                 
K 224    L   104                                                                 
E 225    G   105                                                                 
E 226    D   106                                                                 
TER                                                                              
END                                                                              



