
PFRMAT AL                                                                        
TARGET T0096                                                                     
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  4                                                                         
PARENT 1EUH_B                                                                    
M   1    A   257                                                                 
V   2    I   258                                                                 
I   3    V   259                                                                 
K   4    L   260                                                                 
A   5    E   261                                                                 
Q   6    D   262                                                                 
S   7    A   263                                                                 
P   8    D   264                                                                 
A   9    L   265                                                                 
G  10    E   266                                                                 
F  11    L   267                                                                 
A  12    T   268                                                                 
E  13    A   269                                                                 
E  14    K   270                                                                 
Y  15    N   271                                                                 
I  16    I   272                                                                 
I  17    I   273                                                                 
E  18    A   274                                                                 
S  19    G   275                                                                 
I  20    A   276                                                                 
W  21    S   280                                                                 
N  22    G   281                                                                 
N  23    Q   282                                                                 
R  24    R   283                                                                 
F  25    C   284                                                                 
P  26    T   285                                                                 
P  27    A   286                                                                 
G  28    V   287                                                                 
E  39    K   288                                                                 
L  40    R   289                                                                 
I  41    V   290                                                                 
G  42    L   291                                                                 
V  43    V   292                                                                 
T  44    M   293                                                                 
R  45    E   294                                                                 
T  46    S   295                                                                 
T  47    V   296                                                                 
L  48    A   297                                                                 
R  49    D   298                                                                 
E  50    E   299                                                                 
V  51    L   300                                                                 
L  52    V   301                                                                 
Q  53    E   302                                                                 
R  54    K   303                                                                 
L  55    I   304                                                                 
A  56    R   305                                                                 
D  58    E   306                                                                 
G  59    K   307                                                                 
W  60    V   308                                                                 
L  61    L   309                                                                 
T  62    A   310                                                                 
I  63    L   311                                                                 
Q  64    T   312                                                                 
H  65    I   313                                                                 
G  66    G   314                                                                 
K  67    N   315                                                                 
P  68    P   316                                                                 
T  69    E   317                                                                 
K  70    D   321                                                                 
V  71    I   322                                                                 
N  72    T   323                                                                 
N  73    P   324                                                                 
F  74    L   325                                                                 
W  75    I   326                                                                 
E  76    D   327                                                                 
T  77    T   328                                                                 
S  78    K   329                                                                 
G  79    S   330                                                                 
L  80    A   331                                                                 
N  81    D   332                                                                 
I  82    Y   333                                                                 
L  83    V   334                                                                 
E  84    E   335                                                                 
T  85    G   336                                                                 
L  86    L   337                                                                 
A  87    I   338                                                                 
R  88    N   339                                                                 
L  89    D   340                                                                 
D  90    A   341                                                                 
H  91    N   342                                                                 
E  92    D   343                                                                 
S  93    K   344                                                                 
V  94    G   345                                                                 
P  95    A   346                                                                 
Q  96    T   347                                                                 
L  97    A   348                                                                 
I  98    L   349                                                                 
D  99    T   350                                                                 
N 100    E   351                                                                 
L 101    I   352                                                                 
L 102    K   353                                                                 
S 103    R   354                                                                 
V 104    E   355                                                                 
R 105    G   356                                                                 
T 106    N   357                                                                 
N 107    L   358                                                                 
I 108    I   359                                                                 
S 109    C   360                                                                 
T 110    P   361                                                                 
I 111    I   362                                                                 
F 112    L   363                                                                 
I 113    F   364                                                                 
R 114    D   365                                                                 
T 115    T   369                                                                 
A 116    D   370                                                                 
F 117    M   371                                                                 
R 118    R   372                                                                 
Q 119    L   373                                                                 
H 120    E   377                                                                 
P 121    P   378                                                                 
D 122    F   379                                                                 
K 123    G   380                                                                 
A 124    P   381                                                                 
Q 125    V   382                                                                 
E 126    L   383                                                                 
V 127    P   384                                                                 
L 128    I   385                                                                 
A 129    I   386                                                                 
T 130    R   387                                                                 
A 131    V   388                                                                 
N 132    T   389                                                                 
E 133    S   390                                                                 
V 134    V   391                                                                 
A 135    E   392                                                                 
D 136    E   393                                                                 
H 137    A   394                                                                 
A 138    I   395                                                                 
D 139    E   396                                                                 
A 140    I   397                                                                 
F 141    S   398                                                                 
A 142    N   399                                                                 
E 143    K   400                                                                 
L 144    S   401                                                                 
D 145    E   402                                                                 
Y 146    Y   403                                                                 
N 147    G   404                                                                 
I 148    L   405                                                                 
F 149    Q   406                                                                 
R 177    A   407                                                                 
H 178    S   408                                                                 
Y 179    I   409                                                                 
F 180    F   410                                                                 
A 181    T   411                                                                 
N 182    N   412                                                                 
P 183    D   413                                                                 
E 184    F   414                                                                 
A 185    P   415                                                                 
R 186    R   416                                                                 
S 187    A   417                                                                 
L 188    F   418                                                                 
A 189    G   419                                                                 
L 190    V   426                                                                 
G 191    G   427                                                                 
F 192    T   428                                                                 
Y 193    V   429                                                                 
H 194    H   430                                                                 
K 195    I   431                                                                 
L 196    N   432                                                                 
A 198    N   433                                                                 
L 199    K   434                                                                 
C 200    T   435                                                                 
S 201    Q   436                                                                 
E 202    R   437                                                                 
G 203    G   438                                                                 
A 204    T   439                                                                 
H 205    D   440                                                                 
D 206    N   441                                                                 
Q 207    F   442                                                                 
V 208    P   443                                                                 
Y 209    F   444                                                                 
E 210    L   445                                                                 
T 211    G   446                                                                 
V 212    A   447                                                                 
R 213    K   448                                                                 
R 214    K   449                                                                 
Y 215    S   450                                                                 
G 216    G   451                                                                 
H 217    A   452                                                                 
E 218    G   453                                                                 
S 219    I   454                                                                 
G 220    Q   455                                                                 
E 221    G   456                                                                 
I 222    V   457                                                                 
W 223    K   458                                                                 
H 224    Y   459                                                                 
R 225    S   460                                                                 
M 226    I   461                                                                 
Q 227    E   462                                                                 
K 228    K   475                                                                 
TER                                                                              
END                                                                              



