
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  1                                                                         
PARENT 1B3B_E                                                                    
I  55    L   203                                                                 
P  56    G   204                                                                 
T  57    I   205                                                                 
D  58    D   206                                                                 
P  59    P   207                                                                 
D  60    K   208                                                                 
K  61    K   209                                                                 
N  62    A   210                                                                 
V  63    T   211                                                                 
A  64    V   212                                                                 
G  65    A   213                                                                 
I  66    V   214                                                                 
V  67    Q   215                                                                 
A  68    G   216                                                                 
K  69    F   217                                                                 
K  70    G   218                                                                 
M  71    N   219                                                                 
I  72    V   220                                                                 
D  73    G   221                                                                 
D  74    Q   222                                                                 
F  75    F   223                                                                 
N  76    A   224                                                                 
I  77    A   225                                                                 
G  78    L   226                                                                 
K  82    L   227                                                                 
I  83    I   228                                                                 
T  84    S   229                                                                 
I  85    Q   230                                                                 
K  86    E   231                                                                 
K  87    L   232                                                                 
G  88    G   233                                                                 
V  89    S   234                                                                 
K  90    K   235                                                                 
A  91    V   236                                                                 
G  92    V   237                                                                 
S  93    A   238                                                                 
G  94    V   239                                                                 
L  95    S   240                                                                 
G  96    D   241                                                                 
S  97    S   242                                                                 
S  98    R   243                                                                 
A  99    G   244                                                                 
A 100    G   245                                                                 
S 101    I   246                                                                 
S 102    Y   247                                                                 
A 103    N   248                                                                 
G 104    P   249                                                                 
T 105    E   250                                                                 
A 106    G   251                                                                 
Y 107    F   252                                                                 
A 108    D   253                                                                 
I 109    V   254                                                                 
N 110    E   255                                                                 
E 111    E   256                                                                 
L 112    L   257                                                                 
F 113    I   258                                                                 
K 114    R   259                                                                 
L 115    Y   260                                                                 
N 116    K   261                                                                 
L 117    K   262                                                                 
D 118    E   263                                                                 
K 119    H   264                                                                 
L 120    G   265                                                                 
K 121    T   266                                                                 
L 122    V   267                                                                 
V 123    V   268                                                                 
D 124    T   269                                                                 
Y 125    Y   270                                                                 
A 126    P   271                                                                 
S 127    K   272                                                                 
Y 128    G   273                                                                 
G 129    E   274                                                                 
N 155    R   275                                                                 
Y 156    I   276                                                                 
E 157    T   277                                                                 
P 158    N   278                                                                 
L 159    E   279                                                                 
E 160    E   280                                                                 
V 161    L   281                                                                 
L 162    L   282                                                                 
H 163    E   283                                                                 
I 164    L   284                                                                 
K 169    D   285                                                                 
L 170    V   286                                                                 
D 171    D   287                                                                 
I 172    I   288                                                                 
L 173    L   289                                                                 
I 174    V   290                                                                 
A 175    P   291                                                                 
I 176    A   292                                                                 
P 177    A   293                                                                 
N 178    E   295                                                                 
I 179    G   296                                                                 
S 180    A   297                                                                 
I 181    I   298                                                                 
N 182    H   299                                                                 
T 183    A   300                                                                 
K 184    G   301                                                                 
E 185    N   302                                                                 
A 186    A   303                                                                 
R 187    E   304                                                                 
E 188    R   305                                                                 
I 189    I   306                                                                 
L 190    K   307                                                                 
P 191    A   308                                                                 
K 192    K   309                                                                 
D 198    A   310                                                                 
L 199    V   311                                                                 
V 200    V   312                                                                 
N 201    E   313                                                                 
N 202    G   314                                                                 
V 203    A   315                                                                 
G 204    N   316                                                                 
K 205    G   317                                                                 
A 206    P   318                                                                 
C 207    T   319                                                                 
G 208    T   320                                                                 
M 209    P   321                                                                 
V 210    A   323                                                                 
Y 211    D   324                                                                 
A 212    E   325                                                                 
L 213    I   326                                                                 
Y 214    L   327                                                                 
N 215    S   328                                                                 
K 216    R   329                                                                 
D 217    R   330                                                                 
K 218    G   331                                                                 
S 219    I   332                                                                 
L 220    L   333                                                                 
F 221    V   334                                                                 
G 222    V   335                                                                 
R 223    P   336                                                                 
Y 224    D   337                                                                 
M 225    I   338                                                                 
M 226    L   339                                                                 
S 227    A   340                                                                 
D 228    N   341                                                                 
K 229    A   342                                                                 
G 236    G   343                                                                 
K 237    G   344                                                                 
L 238    V   345                                                                 
I 239    T   346                                                                 
P 240    V   347                                                                 
N 241    S   348                                                                 
Y 242    Y   349                                                                 
F 243    F   350                                                                 
K 244    E   351                                                                 
I 245    W   352                                                                 
K 246    V   353                                                                 
E 247    Q   354                                                                 
E 248    D   355                                                                 
V 249    L   356                                                                 
K 250    Q   357                                                                 
D 251    S   358                                                                 
K 252    F   359                                                                 
V 253    F   360                                                                 
F 268    W   361                                                                 
P 269    D   362                                                                 
K 270    L   363                                                                 
E 271    D   364                                                                 
E 272    Q   365                                                                 
F 273    V   366                                                                 
I 274    R   367                                                                 
D 275    N   368                                                                 
E 276    A   369                                                                 
V 277    L   370                                                                 
E 278    E   371                                                                 
N 279    K   372                                                                 
I 280    M   373                                                                 
L 281    M   374                                                                 
R 282    K   375                                                                 
D 283    K   376                                                                 
Y 284    A   377                                                                 
Y 285    F   378                                                                 
E 286    N   379                                                                 
N 287    D   380                                                                 
T 288    V   381                                                                 
I 289    M   382                                                                 
R 290    K   383                                                                 
TER                                                                              
END                                                                              



