
PFRMAT AL                                                                        
TARGET T0115                                                                     
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  2                                                                         
PARENT 1COW_F                                                                    
V   9    I    82                                                                 
K  10    R    83                                                                 
A  11    I    84                                                                 
P  12    P    85                                                                 
C  13    V    86                                                                 
T  14    G    87                                                                 
S  15    P    88                                                                 
A  16    E    89                                                                 
N  17    T    90                                                                 
L  18    L    91                                                                 
G  19    G    92                                                                 
V  20    R    93                                                                 
G  21    I    94                                                                 
F  22    M    95                                                                 
D  23    N    96                                                                 
V  24    V    97                                                                 
F  25    I    98                                                                 
G  26    G    99                                                                 
L  27    E   100                                                                 
C  28    P   101                                                                 
L  29    I   102                                                                 
K  30    D   103                                                                 
E  31    E   104                                                                 
V  38    R   105                                                                 
E  39    G   106                                                                 
A  40    P   107                                                                 
I  41    I   108                                                                 
D  42    K   109                                                                 
D  43    T   110                                                                 
K  44    K   111                                                                 
E  45    Q   112                                                                 
I  46    F   113                                                                 
I  47    A   114                                                                 
I  48    I   116                                                                 
E  49    H   117                                                                 
V  50    A   118                                                                 
D  51    E   119                                                                 
D  52    A   120                                                                 
K  53    P   121                                                                 
N  54    E   122                                                                 
I  55    M   126                                                                 
P  56    S   127                                                                 
T  57    V   128                                                                 
D  58    E   129                                                                 
P  59    Q   130                                                                 
D  60    E   131                                                                 
K  61    I   132                                                                 
N  62    L   133                                                                 
V  63    V   134                                                                 
A  64    T   135                                                                 
G  65    G   136                                                                 
I  66    I   137                                                                 
V  67    K   138                                                                 
A  68    V   139                                                                 
K  69    V   140                                                                 
K  70    D   141                                                                 
M  71    L   142                                                                 
I  72    L   143                                                                 
D  73    A   144                                                                 
D  74    P   145                                                                 
F  75    Y   146                                                                 
N  76    A   147                                                                 
I  77    K   148                                                                 
G  78    G   149                                                                 
K  79    G   150                                                                 
G  80    K   151                                                                 
V  81    I   152                                                                 
K  82    G   153                                                                 
I  83    L   154                                                                 
T  84    F   155                                                                 
I  85    G   156                                                                 
K  86    G   157                                                                 
S 101    A   158                                                                 
S 102    G   159                                                                 
A 103    V   160                                                                 
G 104    G   161                                                                 
T 105    K   162                                                                 
A 106    T   163                                                                 
Y 107    V   164                                                                 
A 108    L   165                                                                 
I 109    I   166                                                                 
N 110    M   167                                                                 
E 111    E   168                                                                 
L 112    L   169                                                                 
F 113    I   170                                                                 
K 114    N   171                                                                 
L 115    N   172                                                                 
N 116    V   173                                                                 
L 117    A   174                                                                 
A 145    K   175                                                                 
I 146    A   176                                                                 
F 147    H   177                                                                 
G 148    G   178                                                                 
G 149    G   179                                                                 
F 150    Y   180                                                                 
T 151    S   181                                                                 
M 152    V   182                                                                 
L 173    F   183                                                                 
I 174    A   184                                                                 
A 175    G   185                                                                 
I 176    V   186                                                                 
P 177    G   187                                                                 
I 181    E   188                                                                 
N 182    R   189                                                                 
T 183    T   190                                                                 
K 184    R   191                                                                 
E 185    E   192                                                                 
A 186    G   193                                                                 
R 187    N   194                                                                 
E 188    D   195                                                                 
I 189    L   196                                                                 
L 190    Y   197                                                                 
P 191    H   198                                                                 
K 192    G   204                                                                 
A 193    V   205                                                                 
V 194    I   206                                                                 
G 195    N   207                                                                 
L 196    L   208                                                                 
K 197    K   209                                                                 
D 198    D   210                                                                 
L 199    A   211                                                                 
V 200    T   212                                                                 
N 201    S   213                                                                 
N 202    K   214                                                                 
C 207    V   215                                                                 
G 208    A   216                                                                 
M 209    L   217                                                                 
V 210    V   218                                                                 
Y 211    Y   219                                                                 
A 212    G   220                                                                 
L 213    Q   221                                                                 
Y 214    M   222                                                                 
N 215    N   223                                                                 
K 216    E   224                                                                 
D 217    P   225                                                                 
K 218    P   226                                                                 
S 219    G   227                                                                 
L 220    A   228                                                                 
F 221    R   229                                                                 
G 222    A   230                                                                 
R 223    R   231                                                                 
Y 224    V   232                                                                 
M 225    A   233                                                                 
M 226    L   234                                                                 
S 227    T   235                                                                 
D 228    G   236                                                                 
K 229    L   237                                                                 
L 238    T   238                                                                 
I 239    V   239                                                                 
P 240    A   240                                                                 
N 241    E   241                                                                 
Y 242    Y   242                                                                 
F 243    F   243                                                                 
K 244    R   244                                                                 
I 245    D   245                                                                 
K 246    Q   246                                                                 
V 249    E   247                                                                 
K 250    G   248                                                                 
D 251    Q   249                                                                 
K 252    D   250                                                                 
V 253    V   251                                                                 
Y 254    L   252                                                                 
G 255    L   253                                                                 
I 256    F   254                                                                 
T 257    I   255                                                                 
I 258    D   256                                                                 
S 259    N   257                                                                 
I 265    I   258                                                                 
I 266    F   259                                                                 
A 267    R   260                                                                 
F 268    F   261                                                                 
P 269    T   262                                                                 
K 270    Q   263                                                                 
E 271    A   264                                                                 
I 274    G   265                                                                 
D 275    S   266                                                                 
E 276    E   267                                                                 
V 277    V   268                                                                 
E 278    S   269                                                                 
N 279    A   270                                                                 
I 280    L   271                                                                 
L 281    L   272                                                                 
R 282    A   278                                                                 
D 283    V   279                                                                 
Y 284    G   280                                                                 
Y 285    Y   281                                                                 
E 286    Q   282                                                                 
N 287    P   283                                                                 
T 288    T   284                                                                 
I 289    L   285                                                                 
R 290    A   286                                                                 
T 291    T   287                                                                 
E 292    D   288                                                                 
V 293    M   289                                                                 
G 294    G   290                                                                 
K 295    T   291                                                                 
G 296    S   306                                                                 
V 297    V   307                                                                 
E 298    Q   308                                                                 
V 299    A   309                                                                 
V 300    I   310                                                                 
TER                                                                              
END                                                                              



