
PFRMAT AL                                                                        
TARGET T0087                                                                     
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 1DBQ_A                                                                    
I   4    S    61                                                                 
L   5    I    62                                                                 
V   6    G    63                                                                 
F   7    L    64                                                                 
G   8    L    65                                                                 
H   9    A    66                                                                 
Q  10    T    67                                                                 
N  11    S    68                                                                 
P  12    S    69                                                                 
D  13    E    70                                                                 
S  14    A    71                                                                 
M  21    A    72                                                                 
A  22    Y    73                                                                 
Y  23    F    74                                                                 
A  24    A    75                                                                 
Y  25    E    76                                                                 
L  26    I    77                                                                 
K  27    I    78                                                                 
R  28    E    79                                                                 
Q  29    A    80                                                                 
V  32    V    81                                                                 
D  33    E    82                                                                 
A  34    K    83                                                                 
Q  35    N    84                                                                 
A  36    C    85                                                                 
V  37    F    86                                                                 
A  38    Q    87                                                                 
L  39    N    96                                                                 
G  40    A    97                                                                 
N  41    W    98                                                                 
P  42    N    99                                                                 
N  43    N   100                                                                 
E  44    L   101                                                                 
E  45    E   102                                                                 
T  46    K   103                                                                 
A  47    Q   104                                                                 
L  50    R   105                                                                 
D  51    A   106                                                                 
Y  52    Y   107                                                                 
F  53    L   108                                                                 
G  54    S   109                                                                 
S  63    M   110                                                                 
A  64    M   111                                                                 
Q  65    A   112                                                                 
A  66    Q   113                                                                 
E  67    K   114                                                                 
G  68    R   115                                                                 
A  69    V   116                                                                 
K  70    D   117                                                                 
Q  71    G   118                                                                 
V  72    L   119                                                                 
I  73    L   120                                                                 
L  74    V   121                                                                 
T  75    M   122                                                                 
D  76    E   125                                                                 
H  77    Y   126                                                                 
N  78    P   127                                                                 
E  79    E   128                                                                 
F  80    P   129                                                                 
Q  81    L   130                                                                 
Q  82    L   131                                                                 
S  83    A   132                                                                 
I  84    M   133                                                                 
A  85    E   135                                                                 
D  86    E   136                                                                 
I  87    Y   137                                                                 
R  88    R   138                                                                 
E  89    H   139                                                                 
V  90    I   140                                                                 
E  91    P   141                                                                 
V  92    M   142                                                                 
V  93    V   143                                                                 
E  94    V   144                                                                 
V  95    M   145                                                                 
V  96    D   146                                                                 
D  97    W   147                                                                 
H  98    G   148                                                                 
H  99    E   149                                                                 
R 100    A   150                                                                 
T 106    K   151                                                                 
A 107    A   152                                                                 
N 108    D   153                                                                 
P 109    F   154                                                                 
L 110    T   155                                                                 
Y 111    D   156                                                                 
M 112    A   157                                                                 
R 113    V   158                                                                 
L 114    I   159                                                                 
E 115    D   160                                                                 
P 116    N   161                                                                 
V 117    A   162                                                                 
G 118    F   163                                                                 
S 119    E   164                                                                 
A 120    G   165                                                                 
S 121    G   166                                                                 
S 122    Y   167                                                                 
I 123    M   168                                                                 
V 124    A   169                                                                 
Y 125    G   170                                                                 
R 126    R   171                                                                 
L 127    Y   172                                                                 
Y 128    L   173                                                                 
K 129    I   174                                                                 
E 130    E   175                                                                 
N 131    R   176                                                                 
G 132    G   177                                                                 
V 133    H   178                                                                 
S 149    R   179                                                                 
D 150    E   180                                                                 
T 151    I   181                                                                 
L 152    G   182                                                                 
L 153    V   183                                                                 
L 154    I   184                                                                 
K 155    P   185                                                                 
S 156    G   186                                                                 
P 157    P   187                                                                 
P 164    A   194                                                                 
A 165    G   195                                                                 
V 166    R   196                                                                 
A 167    L   197                                                                 
E 168    M   201                                                                 
D 169    K   202                                                                 
L 170    A   203                                                                 
A 171    M   204                                                                 
K 172    E   205                                                                 
I 173    E   206                                                                 
A 174    A   207                                                                 
G 175    M   208                                                                 
V 176    I   209                                                                 
D 177    K   210                                                                 
L 178    V   211                                                                 
Q 179    P   212                                                                 
E 180    E   213                                                                 
M 185    S   214                                                                 
L 186    W   215                                                                 
K 187    I   216                                                                 
A 188    V   217                                                                 
G 189    Q   218                                                                 
T 190    G   219                                                                 
N 191    D   220                                                                 
L 192    F   221                                                                 
A 193    E   222                                                                 
S 194    P   223                                                                 
K 195    E   224                                                                 
T 196    S   225                                                                 
A 197    G   226                                                                 
A 198    Y   227                                                                 
Q 199    R   228                                                                 
L 200    A   229                                                                 
V 201    M   230                                                                 
D 202    Q   231                                                                 
I 203    Q   232                                                                 
F 208    I   233                                                                 
E 209    L   234                                                                 
L 210    S   235                                                                 
N 211    Q   236                                                                 
G 212    P   237                                                                 
S 213    H   238                                                                 
Q 214    R   239                                                                 
V 215    P   240                                                                 
R 216    T   241                                                                 
V 217    A   242                                                                 
A 218    V   243                                                                 
Q 219    F   244                                                                 
V 220    C   245                                                                 
N 221    G   246                                                                 
T 222    G   247                                                                 
V 223    D   248                                                                 
D 224    I   249                                                                 
I 225    M   250                                                                 
N 226    A   251                                                                 
E 227    M   252                                                                 
V 228    G   253                                                                 
L 229    A   254                                                                 
E 236    L   255                                                                 
E 237    C   256                                                                 
A 238    A   257                                                                 
I 239    A   258                                                                 
K 240    D   259                                                                 
A 241    E   260                                                                 
S 242    M   261                                                                 
Q 243    G   262                                                                 
A 244    L   263                                                                 
A 245    R   264                                                                 
N 246    V   265                                                                 
G 247    P   266                                                                 
Y 248    Q   267                                                                 
S 249    D   268                                                                 
D 250    V   269                                                                 
F 251    S   270                                                                 
V 252    L   271                                                                 
L 253    I   272                                                                 
M 254    G   273                                                                 
I 255    Y   274                                                                 
T 256    D   275                                                                 
D 257    N   276                                                                 
I 258    V   277                                                                 
L 259    Y   282                                                                 
N 260    F   283                                                                 
S 261    T   284                                                                 
N 262    P   285                                                                 
S 263    A   286                                                                 
E 264    L   287                                                                 
I 265    T   288                                                                 
L 266    T   289                                                                 
A 267    I   290                                                                 
L 268    H   291                                                                 
G 269    Q   292                                                                 
N 270    P   293                                                                 
N 271    K   294                                                                 
T 272    D   295                                                                 
D 273    S   296                                                                 
K 274    L   297                                                                 
V 275    G   298                                                                 
E 276    E   299                                                                 
A 277    T   300                                                                 
A 278    A   301                                                                 
F 279    F   302                                                                 
N 280    N   303                                                                 
F 281    M   304                                                                 
T 282    L   305                                                                 
H 287    L   306                                                                 
A 288    D   307                                                                 
F 289    R   308                                                                 
L 290    I   309                                                                 
A 291    V   310                                                                 
G 292    N   311                                                                 
A 293    K   312                                                                 
V 294    R   313                                                                 
S 295    E   314                                                                 
R 296    E   315                                                                 
K 297    P   316                                                                 
K 298    Q   317                                                                 
Q 299    E   320                                                                 
V 300    V   321                                                                 
V 301    H   322                                                                 
P 302    P   323                                                                 
Q 303    R   324                                                                 
L 304    L   325                                                                 
T 305    I   326                                                                 
E 306    E   327                                                                 
S 307    R   328                                                                 
F 308    R   329                                                                 
N 309    S   330                                                                 
G 310    V   331                                                                 
TER                                                                              
END                                                                              



