
PFRMAT AL                                                                        
TARGET T0127                                                                     
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 1NSF                                                                      
T   2    K   489                                                                 
T   3    P   490                                                                 
A   4    A   491                                                                 
V   5    F   492                                                                 
A   6    G   493                                                                 
R   7    T   494                                                                 
L   8    N   495                                                                 
Q   9    Q   496                                                                 
P  10    E   497                                                                 
S  11    D   498                                                                 
A  12    Y   499                                                                 
S  13    A   500                                                                 
G  14    S   501                                                                 
A  15    Y   502                                                                 
K  16    I   503                                                                 
T  17    M   504                                                                 
R  18    N   505                                                                 
P  19    G   506                                                                 
V  20    I   507                                                                 
F  21    I   508                                                                 
P  22    K   509                                                                 
F  23    W   510                                                                 
S  24    G   511                                                                 
A  25    D   512                                                                 
I  26    P   513                                                                 
V  27    V   514                                                                 
G  28    T   515                                                                 
Q  29    R   516                                                                 
E  30    V   517                                                                 
D  31    L   518                                                                 
M  32    D   519                                                                 
K  33    D   520                                                                 
L  34    G   521                                                                 
A  35    E   522                                                                 
L  36    L   523                                                                 
L  37    L   524                                                                 
L  38    V   525                                                                 
T  39    Q   526                                                                 
A  40    Q   527                                                                 
V  41    T   528                                                                 
D  42    R   533                                                                 
P  43    T   534                                                                 
G  44    P   535                                                                 
I  45    L   536                                                                 
G  46    V   537                                                                 
G  47    S   538                                                                 
V  48    V   539                                                                 
L  49    L   540                                                                 
V  50    L   541                                                                 
F  51    E   542                                                                 
G  52    G   543                                                                 
D  53    P   544                                                                 
R  54    P   545                                                                 
G  55    H   546                                                                 
T  56    S   547                                                                 
G  57    G   548                                                                 
K  58    K   549                                                                 
R  63    T   550                                                                 
A  64    A   551                                                                 
L  65    L   552                                                                 
A  66    A   553                                                                 
A  67    A   554                                                                 
L  68    K   555                                                                 
L  69    I   556                                                                 
P  70    A   557                                                                 
E  71    E   558                                                                 
I  72    E   559                                                                 
E  73    P   563                                                                 
A  74    F   564                                                                 
V  75    I   565                                                                 
E  76    K   566                                                                 
G  77    I   567                                                                 
C  78    C   568                                                                 
S 114    S   569                                                                 
E 115    P   570                                                                 
D 116    D   571                                                                 
R 117    K   572                                                                 
V 118    M   573                                                                 
V 119    I   574                                                                 
G 120    G   575                                                                 
A 121    F   576                                                                 
L 122    S   577                                                                 
D 123    E   578                                                                 
I 124    T   579                                                                 
E 125    A   580                                                                 
R 126    K   581                                                                 
A 127    C   582                                                                 
I 128    Q   583                                                                 
K 130    A   584                                                                 
G 131    M   585                                                                 
E 132    K   586                                                                 
K 133    K   587                                                                 
A 134    I   588                                                                 
F 135    F   589                                                                 
E 136    D   590                                                                 
P 137    D   591                                                                 
G 138    A   592                                                                 
L 139    Y   593                                                                 
R 142    K   594                                                                 
A 143    S   595                                                                 
N 144    Q   596                                                                 
R 145    L   597                                                                 
G 146    S   598                                                                 
Y 147    C   599                                                                 
L 148    V   600                                                                 
Y 149    V   601                                                                 
I 150    V   602                                                                 
D 151    D   603                                                                 
E 152    D   604                                                                 
C 153    I   605                                                                 
N 154    E   606                                                                 
L 155    R   607                                                                 
L 156    I   614                                                                 
E 157    G   615                                                                 
D 158    P   616                                                                 
H 159    R   617                                                                 
I 160    F   618                                                                 
V 161    S   619                                                                 
D 162    N   620                                                                 
L 163    L   621                                                                 
L 164    V   622                                                                 
L 165    L   623                                                                 
D 166    Q   624                                                                 
V 167    A   625                                                                 
A 168    L   626                                                                 
E 172    L   627                                                                 
N 173    V   628                                                                 
V 174    L   629                                                                 
V 175    L   630                                                                 
E 176    K   631                                                                 
R 177    K   632                                                                 
D 178    A   633                                                                 
G 179    P   634                                                                 
L 180    P   635                                                                 
H 184    Q   636                                                                 
P 185    G   637                                                                 
A 186    R   638                                                                 
R 187    K   639                                                                 
F 188    L   640                                                                 
V 189    L   641                                                                 
L 190    I   642                                                                 
V 191    I   643                                                                 
G 192    G   644                                                                 
S 193    T   645                                                                 
G 194    T   646                                                                 
N 195    S   647                                                                 
P 196    R   648                                                                 
E 197    K   649                                                                 
E 198    D   650                                                                 
G 199    V   651                                                                 
D 200    L   652                                                                 
L 201    Q   653                                                                 
R 202    E   654                                                                 
P 203    M   655                                                                 
Q 204    E   656                                                                 
L 205    M   657                                                                 
L 206    L   658                                                                 
D 207    N   659                                                                 
R 208    A   660                                                                 
F 209    F   661                                                                 
G 210    S   662                                                                 
L 211    T   663                                                                 
S 212    T   664                                                                 
V 213    I   665                                                                 
E 214    H   666                                                                 
V 215    V   667                                                                 
L 216    P   668                                                                 
S 217    N   669                                                                 
P 218    I   670                                                                 
R 219    A   671                                                                 
D 220    T   672                                                                 
V 221    G   673                                                                 
E 222    E   674                                                                 
T 223    Q   675                                                                 
R 224    L   676                                                                 
V 225    L   677                                                                 
E 226    E   678                                                                 
V 227    A   679                                                                 
I 228    L   680                                                                 
R 229    E   681                                                                 
R 230    L   682                                                                 
R 231    L   683                                                                 
D 232    G   684                                                                 
T 233    N   685                                                                 
Y 234    F   686                                                                 
D 235    K   687                                                                 
A 236    D   688                                                                 
D 237    K   689                                                                 
P 238    R   691                                                                 
K 239    T   692                                                                 
A 240    T   693                                                                 
F 241    I   694                                                                 
L 242    A   695                                                                 
E 243    Q   696                                                                 
E 244    Q   697                                                                 
W 245    V   698                                                                 
R 246    K   699                                                                 
P 247    G   700                                                                 
K 248    K   701                                                                 
D 249    K   702                                                                 
M 250    V   703                                                                 
D 251    W   704                                                                 
I 252    I   705                                                                 
R 253    G   706                                                                 
N 254    K   708                                                                 
Q 255    K   709                                                                 
I 256    L   710                                                                 
L 257    L   711                                                                 
E 258    M   712                                                                 
A 259    L   713                                                                 
R 260    I   714                                                                 
E 261    E   715                                                                 
R 262    M   716                                                                 
L 263    S   717                                                                 
P 264    L   718                                                                 
K 265    Q   719                                                                 
V 266    M   720                                                                 
E 267    D   721                                                                 
A 268    P   722                                                                 
P 269    E   723                                                                 
T 271    Y   724                                                                 
A 272    R   725                                                                 
L 273    V   726                                                                 
Y 274    R   727                                                                 
D 275    K   728                                                                 
C 276    F   729                                                                 
A 277    L   730                                                                 
A 278    A   731                                                                 
L 279    L   732                                                                 
C 280    L   733                                                                 
I 281    R   734                                                                 
A 282    E   735                                                                 
TER                                                                              
END                                                                              



