
PFRMAT AL                                                                        
TARGET T0107                                                                     
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 1IGC_H                                                                    
V   1    V     5                                                                 
A   2    E     6                                                                 
T   3    S     7                                                                 
A   4    G     8                                                                 
T   8    G     9                                                                 
P   9    G    10                                                                 
V  10    L    11                                                                 
I  11    V    12                                                                 
D  12    Q    13                                                                 
G  13    P    14                                                                 
E  14    G    15                                                                 
I  15    G    16                                                                 
Y  51    S    17                                                                 
L  52    R    18                                                                 
Y  53    K    19                                                                 
V  54    L    20                                                                 
L  55    S    21                                                                 
A  56    C    22                                                                 
I  57    A    23                                                                 
V  58    A    24                                                                 
K  59    S    25                                                                 
D  60    G    26                                                                 
P  61    F    27                                                                 
P  70    T    28                                                                 
W  71    F    29                                                                 
E  72    S    30                                                                 
Q  73    S    31                                                                 
D  74    F    32                                                                 
S  75    G    33                                                                 
V  76    M    34                                                                 
E  77    H    35                                                                 
I  78    W    36                                                                 
F  79    V    37                                                                 
I  80    R    38                                                                 
D  81    Q    39                                                                 
E  91    A    40                                                                 
D  92    P    41                                                                 
D  93    E    42                                                                 
D  94    K    43                                                                 
A  95    G    44                                                                 
Q  96    L    45                                                                 
F  97    E    46                                                                 
R  98    W    47                                                                 
V  99    V    48                                                                 
N 100    A    49                                                                 
Y 101    Y    50                                                                 
M 102    I    51                                                                 
G 108    S    52                                                                 
T 109    S    53                                                                 
G 110    G    54                                                                 
G 111    S    55                                                                 
S 112    S    56                                                                 
P 113    T    57                                                                 
A 114    L    58                                                                 
R 115    H    59                                                                 
F 116    Y    60                                                                 
K 117    A    61                                                                 
T 118    D    62                                                                 
L 122    T    63                                                                 
I 123    V    64                                                                 
E 124    K    65                                                                 
G 125    G    66                                                                 
G 126    R    67                                                                 
Y 127    F    68                                                                 
I 128    T    69                                                                 
V 129    I    70                                                                 
E 130    S    71                                                                 
I 138    R    72                                                                 
K 139    D    73                                                                 
P 140    N    74                                                                 
T 141    P    75                                                                 
P 142    K    76                                                                 
N 143    N    77                                                                 
T 144    T    78                                                                 
V 145    L    79                                                                 
I 146    F    80                                                                 
I 150    L    81                                                                 
Q 151    Q    82                                                                 
V 152    M    83                                                                 
N 153    T    84                                                                 
D 154    S    85                                                                 
A 155    L    86                                                                 
N 156    R    87                                                                 
E 157    S    88                                                                 
K 158    E    89                                                                 
G 159    D    90                                                                 
Q 160    T    91                                                                 
R 161    G    92                                                                 
V 162    M    93                                                                 
G 163    Y    94                                                                 
I 164    Y    95                                                                 
I 165    C    96                                                                 
S 166    A    97                                                                 
W 167    R    98                                                                 
S 168    W    99                                                                 
D 169    G   100                                                                 
P 170    N   101                                                                 
T 171    Y   102                                                                 
N 172    P   103                                                                 
W 175    Y   104                                                                 
R 176    Y   105                                                                 
D 177    A   106                                                                 
P 178    M   107                                                                 
S 179    D   108                                                                 
K 180    Y   109                                                                 
F 181    W   110                                                                 
G 182    G   111                                                                 
N 183    Q   112                                                                 
L 184    G   113                                                                 
R 185    V   116                                                                 
L 186    T   117                                                                 
I 187    V   118                                                                 
K 188    S   119                                                                 
TER                                                                              
END                                                                              



