
PFRMAT AL                                                                        
TARGET T0128                                                                     
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 1IDS_C                                                                    
K  16    A     2                                                                 
R  17    E     3                                                                 
Y  18    Y     4                                                                 
T  19    T     5                                                                 
L  20    L     6                                                                 
P  21    P     7                                                                 
P  22    D     8                                                                 
L  23    L     9                                                                 
P  24    D    10                                                                 
Y  25    W    11                                                                 
A  26    D    12                                                                 
Y  27    Y    13                                                                 
N  28    G    14                                                                 
A  29    A    15                                                                 
L  30    L    16                                                                 
E  31    E    17                                                                 
P  32    P    18                                                                 
Y  33    H    19                                                                 
I  34    I    20                                                                 
S  35    S    21                                                                 
A  36    G    22                                                                 
E  37    Q    23                                                                 
I  38    I    24                                                                 
M  39    N    25                                                                 
Q  40    E    26                                                                 
L  41    L    27                                                                 
H  42    H    28                                                                 
H  43    H    29                                                                 
Q  44    S    30                                                                 
K  45    K    31                                                                 
H  46    H    32                                                                 
H  47    H    33                                                                 
Q  48    A    34                                                                 
G  49    T    35                                                                 
Y  50    Y    36                                                                 
V  51    V    37                                                                 
N  52    K    38                                                                 
G  53    G    39                                                                 
A  54    A    40                                                                 
N  55    N    41                                                                 
A  56    D    42                                                                 
A  57    A    43                                                                 
L  58    V    44                                                                 
E  59    A    45                                                                 
K  60    K    46                                                                 
L  61    L    47                                                                 
E  62    E    48                                                                 
K  63    E    49                                                                 
F  64    A    50                                                                 
R  65    R    51                                                                 
K  66    A    52                                                                 
G  67    K    53                                                                 
E  68    E    54                                                                 
A  69    D    55                                                                 
Q  70    H    56                                                                 
I  71    S    57                                                                 
D  72    A    58                                                                 
I  73    I    59                                                                 
R  74    L    60                                                                 
A  75    L    61                                                                 
V  76    N    62                                                                 
L  77    E    63                                                                 
R  78    K    64                                                                 
D  79    N    65                                                                 
L  80    L    66                                                                 
S  81    A    67                                                                 
F  82    F    68                                                                 
H  83    N    69                                                                 
L  84    L    70                                                                 
N  85    A    71                                                                 
G  86    G    72                                                                 
H  87    H    73                                                                 
I  88    V    74                                                                 
L  89    N    75                                                                 
H  90    H    76                                                                 
S  91    T    77                                                                 
I  92    I    78                                                                 
F  93    W    79                                                                 
W  94    W    80                                                                 
P  95    K    81                                                                 
N  96    N    82                                                                 
M  97    L    83                                                                 
A  98    S    84                                                                 
P  99    P    85                                                                 
K 102    N    86                                                                 
G 103    G    87                                                                 
G 104    G    88                                                                 
G 105    D    89                                                                 
K 106    K    90                                                                 
P 107    P    91                                                                 
G 108    T    92                                                                 
G 109    G    93                                                                 
K 110    E    94                                                                 
I 111    L    95                                                                 
A 112    A    96                                                                 
D 113    A    97                                                                 
L 114    A    98                                                                 
I 115    I    99                                                                 
N 116    A   100                                                                 
K 117    D   101                                                                 
F 118    A   102                                                                 
F 119    F   103                                                                 
G 120    G   104                                                                 
S 121    S   105                                                                 
F 122    F   106                                                                 
E 123    D   107                                                                 
K 124    K   108                                                                 
F 125    F   109                                                                 
K 126    R   110                                                                 
E 127    A   111                                                                 
E 128    Q   112                                                                 
F 129    F   113                                                                 
S 130    H   114                                                                 
Q 131    A   115                                                                 
A 132    A   116                                                                 
A 133    A   117                                                                 
K 134    T   118                                                                 
N 135    T   119                                                                 
V 136    V   120                                                                 
E 137    Q   121                                                                 
G 138    G   122                                                                 
V 139    S   123                                                                 
G 140    G   124                                                                 
W 141    W   125                                                                 
A 142    A   126                                                                 
I 143    A   127                                                                 
L 144    L   128                                                                 
V 145    G   129                                                                 
Y 146    W   130                                                                 
E 147    D   131                                                                 
P 148    T   132                                                                 
L 149    L   133                                                                 
E 150    G   134                                                                 
E 151    N   135                                                                 
Q 152    K   136                                                                 
L 153    L   137                                                                 
L 154    L   138                                                                 
I 155    I   139                                                                 
L 156    F   140                                                                 
Q 157    Q   141                                                                 
I 158    V   142                                                                 
E 159    Y   143                                                                 
K 160    D   144                                                                 
H 161    H   145                                                                 
N 162    Q   146                                                                 
L 163    T   147                                                                 
M 164    N   148                                                                 
H 165    F   149                                                                 
A 166    P   150                                                                 
A 167    L   151                                                                 
D 168    G   152                                                                 
A 169    I   153                                                                 
Q 170    V   154                                                                 
V 171    P   155                                                                 
L 172    L   156                                                                 
L 173    L   157                                                                 
A 174    L   158                                                                 
L 175    L   159                                                                 
D 176    D   160                                                                 
V 177    M   161                                                                 
W 178    W   162                                                                 
E 179    E   163                                                                 
H 180    H   164                                                                 
A 181    A   165                                                                 
Y 182    F   166                                                                 
Y 183    Y   167                                                                 
L 184    L   168                                                                 
Q 185    Q   169                                                                 
Y 186    Y   170                                                                 
K 187    K   171                                                                 
N 188    N   172                                                                 
D 189    V   173                                                                 
R 190    K   174                                                                 
G 191    V   175                                                                 
S 192    D   176                                                                 
Y 193    F   177                                                                 
V 194    A   178                                                                 
D 195    K   179                                                                 
N 196    A   180                                                                 
W 197    F   181                                                                 
W 198    W   182                                                                 
N 199    N   183                                                                 
V 200    V   184                                                                 
V 201    V   185                                                                 
N 202    N   186                                                                 
W 203    W   187                                                                 
D 204    A   188                                                                 
D 205    D   189                                                                 
V 206    V   190                                                                 
E 207    Q   191                                                                 
R 208    S   192                                                                 
R 209    R   193                                                                 
L 210    Y   194                                                                 
Q 211    A   195                                                                 
K 212    A   196                                                                 
A 213    A   197                                                                 
L 214    T   198                                                                 
N 215    S   199                                                                 
TER                                                                              
END                                                                              



