
PFRMAT AL                                                                        
TARGET T0096                                                                     
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 1DFM_A                                                                    
M   1    L    46                                                                 
V   2    I    47                                                                 
I   3    F    48                                                                 
K   4    D    49                                                                 
A   5    P    50                                                                 
Q   6    V    51                                                                 
S   7    G    52                                                                 
P   8    T    53                                                                 
A   9    N    54                                                                 
G  10    Q    55                                                                 
F  11    Y    56                                                                 
A  12    I    57                                                                 
E  13    K    58                                                                 
E  14    D    59                                                                 
Y  15    E    60                                                                 
I  16    L    61                                                                 
I  17    V    62                                                                 
E  18    P    63                                                                 
S  19    K    64                                                                 
I  20    H    65                                                                 
W  21    W    66                                                                 
N  22    K    67                                                                 
N  23    N    68                                                                 
R  24    N    69                                                                 
F  25    I    70                                                                 
P  32    P    71                                                                 
A  33    I    72                                                                 
E  34    P    73                                                                 
R  35    K    74                                                                 
E  36    R    75                                                                 
L  37    F    76                                                                 
S  38    D    77                                                                 
E  39    F    78                                                                 
L  40    L    79                                                                 
I  41    G    80                                                                 
G  42    T    81                                                                 
V  43    D    82                                                                 
T  44    I    83                                                                 
R  45    D    84                                                                 
T  46    F    85                                                                 
T  47    G    86                                                                 
L  48    K    87                                                                 
R  49    R    88                                                                 
E  50    D    89                                                                 
V  51    T    90                                                                 
L  52    L    91                                                                 
L  61    V    92                                                                 
T  62    E    93                                                                 
I  63    V    94                                                                 
Q  64    Q    95                                                                 
H  65    F    96                                                                 
G  66    S    97                                                                 
K  67    N    98                                                                 
G  79    Y    99                                                                 
L  80    P   100                                                                 
N  81    F   101                                                                 
I  82    L   102                                                                 
L  83    L   103                                                                 
E  84    N   104                                                                 
T  85    N   105                                                                 
L  86    T   106                                                                 
A  87    V   107                                                                 
R  88    E   110                                                                 
L  89    L   111                                                                 
D  90    F   112                                                                 
H  91    H   113                                                                 
E  92    K   114                                                                 
S  93    S   115                                                                 
V  94    N   116                                                                 
Q  96    D   118                                                                 
L  97    I   119                                                                 
I  98    D   120                                                                 
D  99    E   121                                                                 
N 100    E   122                                                                 
L 101    G   123                                                                 
S 103    K   125                                                                 
I 108    V   126                                                                 
S 109    A   127                                                                 
T 110    I   128                                                                 
I 111    I   129                                                                 
F 112    I   130                                                                 
I 113    T   131                                                                 
R 114    K   132                                                                 
T 115    G   133                                                                 
R 118    H   134                                                                 
H 120    F   136                                                                 
P 121    P   137                                                                 
D 122    A   138                                                                 
K 123    S   139                                                                 
A 124    N   140                                                                 
Q 125    S   141                                                                 
E 126    S   142                                                                 
V 127    L   143                                                                 
L 128    Y   144                                                                 
A 129    Y   145                                                                 
T 130    E   146                                                                 
E 133    Q   147                                                                 
V 134    A   148                                                                 
A 135    Q   149                                                                 
D 136    N   150                                                                 
H 137    Q   151                                                                 
A 138    L   152                                                                 
D 139    N   153                                                                 
A 140    S   154                                                                 
F 141    L   155                                                                 
A 142    A   156                                                                 
D 145    E   157                                                                 
Y 146    Y   158                                                                 
N 147    N   159                                                                 
I 148    V   160                                                                 
F 149    F   161                                                                 
R 150    D   162                                                                 
G 151    V   163                                                                 
L 152    E   172                                                                 
A 153    D   173                                                                 
F 154    F   174                                                                 
A 155    E   175                                                                 
S 156    T   176                                                                 
G 157    D   177                                                                 
N 158    I   178                                                                 
P 159    D   179                                                                 
I 160    I   180                                                                 
Y 161    V   181                                                                 
G 162    S   182                                                                 
L 163    T   183                                                                 
I 164    T   184                                                                 
L 165    Y   185                                                                 
N 166    A   186                                                                 
G 167    D   187                                                                 
M 168    K   188                                                                 
K 169    R   189                                                                 
G 170    Y   190                                                                 
L 171    S   191                                                                 
Y 172    R   192                                                                 
T 173    T   193                                                                 
R 174    I   194                                                                 
I 175    T   195                                                                 
G 176    K   196                                                                 
R 177    R   197                                                                 
H 178    D   198                                                                 
Y 179    T   199                                                                 
F 180    T   207                                                                 
A 181    N   208                                                                 
N 182    T   209                                                                 
P 183    P   210                                                                 
E 184    N   211                                                                 
A 185    T   212                                                                 
R 186    R   213                                                                 
S 187    R   214                                                                 
L 188    R   215                                                                 
A 189    K   216                                                                 
L 190    I   220                                                                 
G 191    V   221                                                                 
F 192    T   222                                                                 
Y 193    Y   223                                                                 
TER                                                                              
END                                                                              



