
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  5                                                                         
PARENT 1HGX_A                                                                    
T   8    D     8                                                                 
P   9    D     9                                                                 
V  10    L    10                                                                 
I  11    E    11                                                                 
D  12    R    12                                                                 
G  13    V    13                                                                 
E  14    L    14                                                                 
N  20    Y    15                                                                 
T  21    N    16                                                                 
T  22    Q    17                                                                 
E  23    D    18                                                                 
E  24    D    19                                                                 
I  25    I    20                                                                 
E  26    Q    21                                                                 
R  27    K    22                                                                 
K  28    R    23                                                                 
A  29    I    24                                                                 
V  30    R    25                                                                 
A  31    E    26                                                                 
M  32    L    27                                                                 
G  33    A    28                                                                 
S  34    A    29                                                                 
L  35    E    30                                                                 
D  36    L    31                                                                 
K  37    Y    35                                                                 
N  38    E    36                                                                 
A  39    D    37                                                                 
T  40    K    38                                                                 
A  41    N    39                                                                 
K  42    P    40                                                                 
V  43    V    41                                                                 
R  44    M    42                                                                 
V  45    I    43                                                                 
L  46    C    44                                                                 
W  47    V    45                                                                 
D  48    L    46                                                                 
E  49    T    47                                                                 
N  50    G    48                                                                 
Y  51    A    49                                                                 
L  52    V    50                                                                 
Y  53    F    51                                                                 
V  54    F    52                                                                 
L  55    Y    53                                                                 
A  56    T    54                                                                 
I  57    D    55                                                                 
V  58    L    56                                                                 
K  59    L    57                                                                 
K  65    K    58                                                                 
D  66    H    59                                                                 
N  67    L    60                                                                 
S  68    D    61                                                                 
N  69    F    62                                                                 
P  70    Q    63                                                                 
S  75    L    64                                                                 
V  76    E    65                                                                 
E  77    P    66                                                                 
I  78    D    67                                                                 
F  79    Y    68                                                                 
I  80    I    69                                                                 
D  81    I    70                                                                 
E  82    C    71                                                                 
T  87    S    72                                                                 
G  88    S    73                                                                 
R  98    L    83                                                                 
V  99    T    84                                                                 
N 100    I    85                                                                 
Y 101    S    86                                                                 
M 102    K    87                                                                 
T 106    D    88                                                                 
F 107    L    89                                                                 
G 108    K    90                                                                 
T 109    T    91                                                                 
G 110    N    92                                                                 
G 111    I    93                                                                 
S 112    E    94                                                                 
P 113    G    95                                                                 
A 114    R    96                                                                 
R 115    H    97                                                                 
F 116    V    98                                                                 
K 117    L    99                                                                 
T 118    V   100                                                                 
A 119    V   101                                                                 
V 120    E   102                                                                 
K 121    D   103                                                                 
L 122    I   104                                                                 
I 123    I   105                                                                 
E 124    D   106                                                                 
G 125    T   107                                                                 
G 126    G   108                                                                 
Y 127    L   109                                                                 
I 128    T   110                                                                 
V 129    M   111                                                                 
A 132    Y   112                                                                 
I 133    Q   113                                                                 
K 134    L   114                                                                 
W 135    L   115                                                                 
K 136    N   116                                                                 
T 137    N   117                                                                 
I 138    L   118                                                                 
K 139    Q   119                                                                 
P 140    M   120                                                                 
T 141    R   121                                                                 
P 142    K   122                                                                 
N 143    P   123                                                                 
T 144    A   124                                                                 
V 145    S   125                                                                 
I 146    K   127                                                                 
G 147    V   128                                                                 
F 148    C   129                                                                 
N 149    T   130                                                                 
I 150    L   131                                                                 
Q 151    C   132                                                                 
V 152    D   133                                                                 
N 153    K   134                                                                 
D 154    D   135                                                                 
A 155    I   136                                                                 
N 156    G   137                                                                 
E 157    K   138                                                                 
K 158    K   139                                                                 
G 159    A   140                                                                 
Q 160    Y   141                                                                 
R 161    D   142                                                                 
V 162    R   155                                                                 
G 163    Y   156                                                                 
I 164    I   157                                                                 
I 165    I   158                                                                 
S 166    G   159                                                                 
W 167    Y   160                                                                 
S 168    G   161                                                                 
D 169    F   162                                                                 
P 170    D   163                                                                 
T 171    F   164                                                                 
N 172    H   165                                                                 
N 173    N   166                                                                 
S 174    K   167                                                                 
W 175    Y   168                                                                 
R 176    R   169                                                                 
K 180    N   170                                                                 
F 181    L   171                                                                 
G 182    P   172                                                                 
N 183    V   173                                                                 
L 184    I   174                                                                 
R 185    G   175                                                                 
L 186    I   176                                                                 
I 187    L   177                                                                 
K 188    K   178                                                                 
TER                                                                              
END                                                                              



