
PFRMAT AL                                                                        
TARGET T0113                                                                     
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 1FMC_A                                                                    
M   1    M     1                                                                 
A   2    N     3                                                                 
A   3    S     4                                                                 
A   4    D     5                                                                 
V   5    N     6                                                                 
R   6    L     7                                                                 
S   7    R     8                                                                 
V   8    L     9                                                                 
K   9    D    10                                                                 
G  10    G    11                                                                 
L  11    K    12                                                                 
V  12    C    13                                                                 
A  13    A    14                                                                 
V  14    I    15                                                                 
I  15    I    16                                                                 
T  16    T    17                                                                 
G  17    G    18                                                                 
G  18    A    19                                                                 
A  19    G    20                                                                 
S  20    A    21                                                                 
G  21    G    22                                                                 
L  22    I    23                                                                 
G  23    G    24                                                                 
L  24    K    25                                                                 
S  25    E    26                                                                 
T  26    I    27                                                                 
A  27    A    28                                                                 
K  28    I    29                                                                 
R  29    T    30                                                                 
L  30    F    31                                                                 
V  31    A    32                                                                 
G  32    T    33                                                                 
Q  33    A    34                                                                 
G  34    G    35                                                                 
A  35    A    36                                                                 
T  36    S    37                                                                 
A  37    V    38                                                                 
V  38    V    39                                                                 
L  39    V    40                                                                 
L  40    S    41                                                                 
D  41    D    42                                                                 
V  42    I    43                                                                 
P  43    A    47                                                                 
N  44    A    48                                                                 
S  45    N    49                                                                 
E  46    H    50                                                                 
G  47    V    51                                                                 
E  48    V    52                                                                 
T  49    D    53                                                                 
E  50    E    54                                                                 
A  51    I    55                                                                 
K  52    Q    56                                                                 
K  53    Q    57                                                                 
L  54    L    58                                                                 
G  55    G    59                                                                 
G  56    G    60                                                                 
N  57    Q    61                                                                 
C  58    A    62                                                                 
I  59    F    63                                                                 
F  60    A    64                                                                 
A  61    C    65                                                                 
P  62    R    66                                                                 
A  63    C    67                                                                 
N  64    D    68                                                                 
V  65    I    69                                                                 
T  66    T    70                                                                 
S  67    S    71                                                                 
E  68    E    72                                                                 
K  69    Q    73                                                                 
E  70    E    74                                                                 
V  71    L    75                                                                 
Q  72    S    76                                                                 
A  73    A    77                                                                 
A  74    L    78                                                                 
L  75    A    79                                                                 
T  76    D    80                                                                 
L  77    F    81                                                                 
A  78    A    82                                                                 
K  79    I    83                                                                 
E  80    S    84                                                                 
K  81    K    85                                                                 
F  82    L    86                                                                 
G  83    G    87                                                                 
R  84    K    88                                                                 
I  85    V    89                                                                 
D  86    D    90                                                                 
V  87    I    91                                                                 
A  88    L    92                                                                 
V  89    V    93                                                                 
N  90    N    94                                                                 
C  91    N    95                                                                 
A  92    A    96                                                                 
G  93    G    97                                                                 
I  94    G    98                                                                 
A  95    G    99                                                                 
V  96    G   100                                                                 
I  98    P   101                                                                 
K  99    K   102                                                                 
T 100    P   103                                                                 
Y 101    F   104                                                                 
H 102    D   105                                                                 
E 103    M   106                                                                 
K 104    P   107                                                                 
L 111    M   108                                                                 
E 112    A   109                                                                 
D 113    D   110                                                                 
F 114    F   111                                                                 
Q 115    R   112                                                                 
R 116    R   113                                                                 
V 117    A   114                                                                 
I 118    Y   115                                                                 
N 119    E   116                                                                 
V 120    L   117                                                                 
N 121    N   118                                                                 
L 122    V   119                                                                 
I 123    F   120                                                                 
G 124    S   121                                                                 
T 125    F   122                                                                 
F 126    F   123                                                                 
N 127    H   124                                                                 
V 128    L   125                                                                 
I 129    S   126                                                                 
R 130    Q   127                                                                 
L 131    L   128                                                                 
V 132    V   129                                                                 
A 133    A   130                                                                 
G 134    P   131                                                                 
V 135    E   132                                                                 
M 136    M   133                                                                 
G 137    E   134                                                                 
Q 138    K   135                                                                 
N 139    N   136                                                                 
E 140    G   137                                                                 
P 141    G   138                                                                 
G 148    G   139                                                                 
V 149    V   140                                                                 
I 150    I   141                                                                 
I 151    L   142                                                                 
N 152    T   143                                                                 
T 153    I   144                                                                 
A 154    T   145                                                                 
S 155    S   146                                                                 
V 156    M   147                                                                 
A 157    A   148                                                                 
A 158    A   149                                                                 
F 159    E   150                                                                 
E 160    N   151                                                                 
G 161    K   152                                                                 
Q 162    N   153                                                                 
V 163    I   154                                                                 
G 164    N   155                                                                 
Q 165    M   156                                                                 
A 166    T   157                                                                 
A 167    S   158                                                                 
Y 168    Y   159                                                                 
S 169    A   160                                                                 
A 170    S   161                                                                 
S 171    S   162                                                                 
K 172    K   163                                                                 
G 173    A   164                                                                 
G 174    A   165                                                                 
I 175    A   166                                                                 
V 176    S   167                                                                 
G 177    H   168                                                                 
M 178    L   169                                                                 
T 179    V   170                                                                 
L 180    R   171                                                                 
P 181    N   172                                                                 
I 182    M   173                                                                 
A 183    A   174                                                                 
R 184    F   175                                                                 
D 185    D   176                                                                 
L 186    L   177                                                                 
A 187    G   178                                                                 
P 188    E   179                                                                 
I 189    K   180                                                                 
G 190    N   181                                                                 
I 191    I   182                                                                 
R 192    R   183                                                                 
V 193    V   184                                                                 
V 194    N   185                                                                 
T 195    G   186                                                                 
I 196    I   187                                                                 
A 197    A   188                                                                 
P 198    P   189                                                                 
G 199    G   190                                                                 
L 200    A   191                                                                 
F 201    I   192                                                                 
A 202    L   193                                                                 
T 203    T   194                                                                 
P 204    D   195                                                                 
L 205    A   196                                                                 
L 206    L   197                                                                 
T 207    K   198                                                                 
T 208    S   199                                                                 
L 209    V   200                                                                 
P 210    T   202                                                                 
D 211    P   203                                                                 
K 212    E   204                                                                 
V 213    I   205                                                                 
R 214    E   206                                                                 
N 215    Q   207                                                                 
F 216    K   208                                                                 
L 217    M   209                                                                 
A 218    L   210                                                                 
S 219    Q   211                                                                 
Q 220    H   212                                                                 
V 221    T   213                                                                 
P 222    P   214                                                                 
F 223    I   215                                                                 
S 225    R   216                                                                 
R 226    R   217                                                                 
L 227    L   218                                                                 
G 228    G   219                                                                 
D 229    Q   220                                                                 
P 230    P   221                                                                 
A 231    Q   222                                                                 
E 232    D   223                                                                 
Y 233    I   224                                                                 
A 234    A   225                                                                 
H 235    N   226                                                                 
L 236    A   227                                                                 
V 237    A   228                                                                 
Q 238    L   229                                                                 
M 239    F   230                                                                 
V 240    L   231                                                                 
I 241    C   232                                                                 
E 242    A   235                                                                 
N 243    A   236                                                                 
P 244    S   237                                                                 
F 245    W   238                                                                 
L 246    V   239                                                                 
N 247    S   240                                                                 
G 248    G   241                                                                 
E 249    Q   242                                                                 
V 250    I   243                                                                 
I 251    L   244                                                                 
R 252    T   245                                                                 
L 253    V   246                                                                 
D 254    S   247                                                                 
G 255    G   248                                                                 
A 256    G   249                                                                 
I 257    V   251                                                                 
R 258    Q   252                                                                 
M 259    E   253                                                                 
Q 260    L   254                                                                 
P 261    N   255                                                                 
TER                                                                              
END                                                                              



