
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  4                                                                         
PARENT 1DHF_A                                                                    
V   1    C     6                                                                 
A   2    I     7                                                                 
T   3    V     8                                                                 
A   4    A     9                                                                 
K   5    V    10                                                                 
Y   6    S    11                                                                 
G   7    Q    12                                                                 
T   8    N    13                                                                 
P   9    M    14                                                                 
V  10    G    15                                                                 
I  11    I    16                                                                 
D  12    G    17                                                                 
G  13    K    18                                                                 
E  14    N    19                                                                 
I  15    G    20                                                                 
D  16    D    21                                                                 
E  17    L    22                                                                 
I  18    P    23                                                                 
W  19    W    24                                                                 
N  20    P    25                                                                 
T  21    P    26                                                                 
T  22    L    27                                                                 
E  23    R    28                                                                 
E  24    N    29                                                                 
I  25    E    30                                                                 
E  26    F    31                                                                 
R  27    F    34                                                                 
K  28    Q    35                                                                 
A  29    R    36                                                                 
V  30    M    37                                                                 
A  31    T    38                                                                 
M  32    T    39                                                                 
G  33    T    40                                                                 
S  34    S    41                                                                 
L  35    S    42                                                                 
D  36    V    43                                                                 
K  37    E    44                                                                 
N  38    G    45                                                                 
A  39    K    46                                                                 
T  40    Q    47                                                                 
A  41    N    48                                                                 
K  42    L    49                                                                 
V  43    V    50                                                                 
R  44    I    51                                                                 
Y  53    M    52                                                                 
V  54    G    53                                                                 
L  55    K    54                                                                 
A  56    K    55                                                                 
I  57    T    56                                                                 
V  58    W    57                                                                 
K  59    F    58                                                                 
D  60    S    59                                                                 
P  61    I    60                                                                 
V  62    P    61                                                                 
L  63    E    62                                                                 
N  64    K    63                                                                 
K  65    N    64                                                                 
D  66    R    65                                                                 
N  67    P    66                                                                 
S  68    L    67                                                                 
N  69    K    68                                                                 
P  70    G    69                                                                 
S  75    R    70                                                                 
V  76    I    71                                                                 
E  77    N    72                                                                 
I  78    L    73                                                                 
F  79    V    74                                                                 
I  80    L    75                                                                 
D  81    S    76                                                                 
E  82    R    77                                                                 
N  83    E    78                                                                 
N  84    L    79                                                                 
H  85    K    80                                                                 
K  86    E    81                                                                 
T  87    P    82                                                                 
G  88    P    83                                                                 
D  93    Q    84                                                                 
D  94    G    85                                                                 
A  95    A    86                                                                 
Q  96    H    87                                                                 
F  97    F    88                                                                 
R  98    L    89                                                                 
V  99    S    90                                                                 
N 100    R    91                                                                 
Y 101    S    92                                                                 
M 102    L    93                                                                 
N 103    D    94                                                                 
E 104    D    95                                                                 
Q 105    A    96                                                                 
F 107    L    97                                                                 
G 108    K    98                                                                 
T 109    L    99                                                                 
G 110    T   100                                                                 
G 111    E   101                                                                 
S 112    Q   102                                                                 
P 113    P   103                                                                 
A 114    E   104                                                                 
R 115    L   105                                                                 
F 116    A   106                                                                 
K 117    N   107                                                                 
T 118    K   108                                                                 
A 119    V   109                                                                 
V 120    D   110                                                                 
K 121    M   111                                                                 
L 122    V   112                                                                 
I 123    W   113                                                                 
E 124    I   114                                                                 
G 125    V   115                                                                 
G 126    G   116                                                                 
I 128    G   117                                                                 
V 129    S   118                                                                 
E 130    S   119                                                                 
A 131    V   120                                                                 
A 132    Y   121                                                                 
I 133    K   122                                                                 
K 134    E   123                                                                 
I 138    A   124                                                                 
K 139    M   125                                                                 
P 140    N   126                                                                 
T 141    H   127                                                                 
P 142    P   128                                                                 
N 143    G   129                                                                 
T 144    H   130                                                                 
V 145    L   131                                                                 
I 146    K   132                                                                 
G 147    L   133                                                                 
F 148    F   134                                                                 
N 149    V   135                                                                 
I 150    T   136                                                                 
Q 151    R   137                                                                 
V 152    I   138                                                                 
N 153    M   139                                                                 
D 154    Q   140                                                                 
A 155    D   141                                                                 
N 156    F   142                                                                 
R 161    E   143                                                                 
V 162    S   144                                                                 
G 163    D   145                                                                 
I 164    T   146                                                                 
I 165    F   147                                                                 
S 166    F   148                                                                 
W 167    P   149                                                                 
S 168    E   150                                                                 
D 169    I   151                                                                 
P 170    D   152                                                                 
T 171    L   153                                                                 
N 172    E   154                                                                 
N 173    K   155                                                                 
S 174    Y   156                                                                 
W 175    K   157                                                                 
R 176    L   158                                                                 
D 177    L   159                                                                 
P 178    V   169                                                                 
S 179    Q   170                                                                 
K 180    E   171                                                                 
F 181    E   172                                                                 
G 182    K   173                                                                 
N 183    G   174                                                                 
L 184    I   175                                                                 
R 185    K   176                                                                 
L 186    E   183                                                                 
I 187    K   184                                                                 
K 188    N   185                                                                 
TER                                                                              
END                                                                              



