
PFRMAT AL                                                                        
TARGET T0126                                                                     
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 2OTC_B                                                                    
K   8    K   151                                                                 
Q   9    A   152                                                                 
Q  10    F   153                                                                 
L  11    N   154                                                                 
E  12    E   155                                                                 
M  13    M   156                                                                 
P  14    T   157                                                                 
L  15    L   158                                                                 
V  16    V   159                                                                 
L  17    Y   160                                                                 
D  18    A   161                                                                 
Q  19    G   162                                                                 
D  20    D   163                                                                 
L  21    A   164                                                                 
T  22    R   165                                                                 
Q  23    N   166                                                                 
Q  24    N   167                                                                 
M  25    M   168                                                                 
R  26    G   169                                                                 
L  27    N   170                                                                 
S  31    S   171                                                                 
L  32    M   172                                                                 
K  33    L   173                                                                 
Q  34    E   174                                                                 
R  35    A   175                                                                 
G  36    A   176                                                                 
E  37    A   177                                                                 
K  38    L   178                                                                 
K  39    T   179                                                                 
Q  40    G   180                                                                 
D  41    L   181                                                                 
G  42    D   182                                                                 
E  43    L   183                                                                 
K  44    R   184                                                                 
L  45    L   185                                                                 
I  46    V   186                                                                 
R  47    A   187                                                                 
P  48    P   188                                                                 
A  49    Q   189                                                                 
E  50    A   190                                                                 
S  51    C   191                                                                 
I  58    W   192                                                                 
Q  59    P   193                                                                 
Q  60    E   194                                                                 
Q  61    A   195                                                                 
K  62    A   196                                                                 
L  63    L   197                                                                 
Q  64    V   198                                                                 
F  65    T   199                                                                 
D  66    E   200                                                                 
H  67    C   201                                                                 
W  68    R   202                                                                 
N  69    A   203                                                                 
V  70    L   204                                                                 
V  71    A   205                                                                 
L  72    Q   206                                                                 
D  73    Q   207                                                                 
K  74    N   208                                                                 
P  75    G   209                                                                 
G  76    G   210                                                                 
K  77    N   211                                                                 
V  78    I   212                                                                 
T  79    T   213                                                                 
I  80    L   214                                                                 
T  81    T   215                                                                 
N  93    E   216                                                                 
L  94    D   217                                                                 
M  95    V   218                                                                 
T  96    A   219                                                                 
R  97    K   220                                                                 
Q  98    G   221                                                                 
L  99    V   222                                                                 
L 100    E   223                                                                 
D 101    G   224                                                                 
P 102    A   225                                                                 
A 103    D   226                                                                 
A 104    F   227                                                                 
I 105    I   228                                                                 
F 106    V   232                                                                 
W 107    W   233                                                                 
R 108    V   234                                                                 
K 109    S   235                                                                 
E 110    M   236                                                                 
D 111    G   237                                                                 
S 112    E   238                                                                 
D 113    A   239                                                                 
A 114    K   240                                                                 
M 115    E   241                                                                 
D 116    K   242                                                                 
W 117    W   243                                                                 
N 118    A   244                                                                 
E 119    E   245                                                                 
A 120    R   246                                                                 
D 121    I   247                                                                 
A 122    A   248                                                                 
L 123    Y   253                                                                 
E 124    Q   254                                                                 
F 125    V   255                                                                 
G 126    N   256                                                                 
E 127    S   257                                                                 
R 128    K   258                                                                 
L 129    M   259                                                                 
S 130    M   260                                                                 
D 131    Q   261                                                                 
L 132    L   262                                                                 
A 133    T   263                                                                 
K 134    G   264                                                                 
I 135    N   265                                                                 
R 136    P   266                                                                 
K 137    E   267                                                                 
V 138    V   268                                                                 
M 139    K   269                                                                 
Y 140    F   270                                                                 
F 141    L   271                                                                 
L 142    L   274                                                                 
I 143    P   275                                                                 
T 144    A   276                                                                 
F 145    F   277                                                                 
G 146    H   278                                                                 
E 147    D   279                                                                 
G 148    D   280                                                                 
V 149    Q   281                                                                 
E 150    T   282                                                                 
P 151    T   283                                                                 
A 152    L   284                                                                 
N 153    G   285                                                                 
L 154    K   286                                                                 
K 155    K   287                                                                 
A 156    M   288                                                                 
S 157    A   289                                                                 
V 158    E   290                                                                 
V 159    V   300                                                                 
F 160    T   301                                                                 
N 161    D   302                                                                 
Q 162    E   303                                                                 
L 163    V   304                                                                 
TER                                                                              
END                                                                              



