
PFRMAT AL                                                                        
TARGET T0104                                                                     
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  3                                                                         
PARENT 9ATC_A                                                                    
M   1    L   152                                                                 
E   2    D   153                                                                 
S   3    N   154                                                                 
L   4    L   155                                                                 
T   5    H   156                                                                 
Q   6    V   157                                                                 
Y   7    A   158                                                                 
I   8    M   159                                                                 
P   9    V   160                                                                 
D  10    G   161                                                                 
M  14    D   162                                                                 
L  15    L   163                                                                 
R  16    K   164                                                                 
F  17    F   165                                                                 
G  18    G   166                                                                 
K  19    R   167                                                                 
K  20    T   168                                                                 
F  21    V   169                                                                 
A  22    T   173                                                                 
E  23    Q   174                                                                 
I  24    A   175                                                                 
L  25    L   176                                                                 
L  26    A   177                                                                 
K  27    K   178                                                                 
L  28    F   179                                                                 
H  29    D   180                                                                 
T  30    G   181                                                                 
E  31    N   182                                                                 
I  34    R   183                                                                 
M  35    F   184                                                                 
V  36    Y   185                                                                 
Y  37    F   186                                                                 
L  38    I   187                                                                 
N  39    A   188                                                                 
G  40    P   189                                                                 
G  45    D   190                                                                 
K  46    A   191                                                                 
T  47    L   192                                                                 
T  48    A   193                                                                 
L  49    M   194                                                                 
T  50    P   195                                                                 
R  51    Q   196                                                                 
G  52    Y   197                                                                 
M  53    I   198                                                                 
L  54    L   199                                                                 
Q  55    D   200                                                                 
G  56    M   201                                                                 
I  57    L   202                                                                 
G  58    D   203                                                                 
Q  60    E   204                                                                 
G  61    K   205                                                                 
N  62    G   206                                                                 
V  63    I   207                                                                 
K  64    A   208                                                                 
S  65    W   209                                                                 
P  66    S   210                                                                 
T  67    L   211                                                                 
Y  68    H   212                                                                 
T  69    S   213                                                                 
L  70    S   214                                                                 
V  71    I   215                                                                 
E  72    E   216                                                                 
E  73    E   217                                                                 
Y  74    V   218                                                                 
N  75    M   219                                                                 
I  76    A   220                                                                 
A  77    E   221                                                                 
G  78    V   222                                                                 
K  79    D   223                                                                 
M  80    I   224                                                                 
I  81    L   225                                                                 
Y  82    Y   226                                                                 
H  83    M   227                                                                 
F  84    T   228                                                                 
D  85    R   229                                                                 
L  86    V   230                                                                 
Y  87    Q   231                                                                 
R  88    K   232                                                                 
A  90    E   233                                                                 
D  91    R   234                                                                 
P  92    L   235                                                                 
E  93    D   236                                                                 
E  94    P   237                                                                 
L  95    S   238                                                                 
E  96    E   239                                                                 
F  97    Y   240                                                                 
M  98    A   241                                                                 
G  99    N   242                                                                 
I 100    V   243                                                                 
R 101    K   244                                                                 
D 102    A   245                                                                 
Y 103    Q   246                                                                 
F 104    F   247                                                                 
N 105    V   248                                                                 
T 106    L   249                                                                 
D 107    R   250                                                                 
S 108    N   260                                                                 
I 109    M   261                                                                 
C 110    K   262                                                                 
L 111    V   263                                                                 
I 112    L   264                                                                 
E 113    H   265                                                                 
W 114    P   266                                                                 
S 115    L   267                                                                 
E 116    P   268                                                                 
K 117    R   269                                                                 
G 118    V   270                                                                 
Q 119    D   271                                                                 
G 120    E   272                                                                 
I 121    I   273                                                                 
L 122    A   274                                                                 
P 123    T   275                                                                 
E 124    D   276                                                                 
A 125    V   277                                                                 
D 126    D   278                                                                 
I 127    K   279                                                                 
L 128    T   280                                                                 
V 129    P   281                                                                 
N 130    H   282                                                                 
I 131    A   283                                                                 
D 132    W   284                                                                 
Y 133    Y   285                                                                 
Y 134    F   286                                                                 
D 135    Q   287                                                                 
D 136    Q   288                                                                 
A 137    A   289                                                                 
R 138    G   290                                                                 
N 139    N   291                                                                 
I 140    G   292                                                                 
E 141    I   293                                                                 
L 142    F   294                                                                 
I 143    A   295                                                                 
A 144    R   296                                                                 
Q 145    Q   297                                                                 
T 146    A   298                                                                 
N 147    L   299                                                                 
L 148    L   300                                                                 
G 149    A   301                                                                 
K 150    L   302                                                                 
N 151    V   303                                                                 
I 152    L   304                                                                 
I 153    N   305                                                                 
S 154    R   306                                                                 
A 155    D   307                                                                 
F 156    L   308                                                                 
S 157    V   309                                                                 
N 158    L   310                                                                 
TER                                                                              
END                                                                              



