
PFRMAT AL                                                                        
TARGET T0126                                                                     
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 1A8V_A                                                                    
M   1    L     3                                                                 
A   2    T     4                                                                 
E   3    K     7                                                                 
D   4    N     8                                                                 
G   5    T     9                                                                 
P   6    P    10                                                                 
Q   7    V    11                                                                 
K   8    S    12                                                                 
Q   9    E    13                                                                 
Q  10    L    14                                                                 
L  11    I    15                                                                 
E  12    T    16                                                                 
L  15    L    17                                                                 
V  16    G    18                                                                 
L  17    E    19                                                                 
D  18    N    20                                                                 
Q  19    M    21                                                                 
D  20    G    22                                                                 
L  21    L    23                                                                 
T  22    E    24                                                                 
Q  23    N    25                                                                 
Q  24    L    26                                                                 
M  25    A    27                                                                 
R  26    R    28                                                                 
L  27    M    29                                                                 
R  28    R    30                                                                 
V  29    K    31                                                                 
E  30    Q    32                                                                 
S  31    D    33                                                                 
L  32    I    34                                                                 
K  33    I    35                                                                 
Q  34    F    36                                                                 
R  35    A    37                                                                 
G  36    I    38                                                                 
E  37    L    39                                                                 
K  38    K    40                                                                 
K  39    Q    41                                                                 
Q  40    H    42                                                                 
I  46    A    43                                                                 
R  47    K    44                                                                 
P  48    S    45                                                                 
A  49    G    46                                                                 
E  50    E    47                                                                 
S  51    D    48                                                                 
V  52    I    49                                                                 
Y  53    F    50                                                                 
R  54    G    51                                                                 
L  55    D    52                                                                 
W  68    G    53                                                                 
N  69    V    54                                                                 
V  70    L    55                                                                 
V  71    E    56                                                                 
L  72    I    57                                                                 
D  73    L    58                                                                 
K  74    Q    59                                                                 
P  75    D    60                                                                 
G  76    G    61                                                                 
K  77    F    62                                                                 
V  78    G    63                                                                 
T  79    F    64                                                                 
I  80    L    65                                                                 
T  81    R    66                                                                 
G  82    S    67                                                                 
T  83    A    68                                                                 
L 100    A    74                                                                 
D 101    G    75                                                                 
P 102    P    76                                                                 
A 103    D    77                                                                 
A 104    D    78                                                                 
I 105    I    79                                                                 
F 106    Y    80                                                                 
W 107    V    81                                                                 
R 108    S    82                                                                 
K 109    P    83                                                                 
E 110    S    84                                                                 
D 111    Q    85                                                                 
S 112    I    86                                                                 
D 113    R    87                                                                 
A 114    R    88                                                                 
M 115    F    89                                                                 
A 122    N    90                                                                 
L 123    L    91                                                                 
E 124    R    92                                                                 
F 125    T    93                                                                 
G 126    G    94                                                                 
E 127    D    95                                                                 
R 128    T    96                                                                 
L 129    I    97                                                                 
S 130    S    98                                                                 
D 131    G    99                                                                 
L 132    K   100                                                                 
A 133    I   101                                                                 
K 134    R   102                                                                 
I 135    P   103                                                                 
R 136    P   104                                                                 
K 137    E   108                                                                 
V 138    R   109                                                                 
M 139    Y   110                                                                 
Y 140    F   111                                                                 
F 141    A   112                                                                 
L 142    L   113                                                                 
I 143    L   114                                                                 
T 144    K   115                                                                 
F 145    V   116                                                                 
G 146    N   117                                                                 
E 147    E   118                                                                 
TER                                                                              
END                                                                              



