
PFRMAT AL                                                                        
TARGET T0121                                                                     
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 1B0U_A                                                                    
V   4    N     5                                                                 
R   5    K     6                                                                 
L   6    L     7                                                                 
V   7    I    10                                                                 
D   8    D    11                                                                 
V   9    L    12                                                                 
W  10    H    13                                                                 
K  11    K    14                                                                 
V  12    R    15                                                                 
F  13    Y    16                                                                 
G  14    G    17                                                                 
E  15    G    18                                                                 
V  16    H    19                                                                 
T  17    E    20                                                                 
A  18    V    21                                                                 
V  19    L    22                                                                 
R  20    K    23                                                                 
E  21    G    24                                                                 
L  22    V    25                                                                 
S  23    S    26                                                                 
L  24    L    27                                                                 
E  25    Q    28                                                                 
V  26    A    29                                                                 
K  27    R    30                                                                 
D  28    A    31                                                                 
G  29    G    32                                                                 
E  30    D    33                                                                 
F  31    V    34                                                                 
M  32    I    35                                                                 
I  33    S    36                                                                 
L  34    I    37                                                                 
L  35    I    38                                                                 
G  36    G    39                                                                 
P  37    S    40                                                                 
S  38    S    41                                                                 
G  39    G    42                                                                 
C  40    S    43                                                                 
G  41    G    44                                                                 
K  42    K    45                                                                 
T  43    S    46                                                                 
T  44    T    47                                                                 
T  45    F    48                                                                 
L  46    L    49                                                                 
R  47    R    50                                                                 
M  48    C    51                                                                 
I  49    I    52                                                                 
A  50    N    53                                                                 
G  51    F    54                                                                 
L  52    L    55                                                                 
E  53    E    56                                                                 
E  54    K    57                                                                 
P  55    P    58                                                                 
S  56    S    59                                                                 
R  57    E    60                                                                 
G  58    G    61                                                                 
Q  59    A    62                                                                 
I  60    I    63                                                                 
Y  61    I    64                                                                 
I  62    V    65                                                                 
G  63    N    66                                                                 
D  64    G    67                                                                 
R  65    Q    68                                                                 
L  66    L    72                                                                 
V  67    V    73                                                                 
A  68    R    74                                                                 
D  69    D    75                                                                 
P  70    K    76                                                                 
E  71    D    77                                                                 
K  72    G    78                                                                 
G  73    Q    79                                                                 
I  74    L    80                                                                 
F  75    K    81                                                                 
V  76    V    82                                                                 
P  77    A    83                                                                 
P  78    D    84                                                                 
K  79    K    85                                                                 
D  80    N    86                                                                 
R  81    Q    87                                                                 
D  82    R    94                                                                 
I  83    L    95                                                                 
A  84    T    96                                                                 
M  85    M    97                                                                 
V  86    V    98                                                                 
F  87    F    99                                                                 
Q  88    Q   100                                                                 
S  89    H   101                                                                 
Y  90    F   102                                                                 
A  91    N   103                                                                 
L  92    L   104                                                                 
Y  93    W   105                                                                 
P  94    S   106                                                                 
H  95    H   107                                                                 
M  96    M   108                                                                 
T  97    T   109                                                                 
V  98    V   110                                                                 
Y  99    L   111                                                                 
D 100    E   112                                                                 
N 101    N   113                                                                 
I 102    V   114                                                                 
A 103    E   116                                                                 
F 104    A   117                                                                 
P 105    P   118                                                                 
L 106    I   119                                                                 
K 107    Q   120                                                                 
L 108    V   121                                                                 
R 109    L   122                                                                 
K 110    G   123                                                                 
V 111    L   124                                                                 
P 112    S   125                                                                 
R 113    K   126                                                                 
Q 114    H   127                                                                 
E 115    D   128                                                                 
I 116    A   129                                                                 
D 117    R   130                                                                 
Q 118    E   131                                                                 
R 119    R   132                                                                 
V 120    A   133                                                                 
R 121    L   134                                                                 
E 122    K   135                                                                 
V 123    Y   136                                                                 
A 124    L   137                                                                 
E 125    A   138                                                                 
L 126    K   139                                                                 
L 127    V   140                                                                 
G 128    G   141                                                                 
L 129    I   142                                                                 
T 130    D   143                                                                 
E 131    E   144                                                                 
L 132    R   145                                                                 
L 133    A   146                                                                 
N 134    Q   147                                                                 
R 135    G   148                                                                 
K 136    K   149                                                                 
P 137    P   151                                                                 
R 138    V   152                                                                 
E 139    H   153                                                                 
L 140    L   154                                                                 
S 141    S   155                                                                 
G 142    G   156                                                                 
G 143    G   157                                                                 
Q 144    Q   158                                                                 
R 145    Q   159                                                                 
Q 146    Q   160                                                                 
R 147    R   161                                                                 
V 148    V   162                                                                 
A 149    S   163                                                                 
L 150    I   164                                                                 
G 151    A   165                                                                 
R 152    R   166                                                                 
A 153    A   167                                                                 
I 154    L   168                                                                 
V 155    A   169                                                                 
R 156    M   170                                                                 
K 157    E   171                                                                 
P 158    P   172                                                                 
Q 159    D   173                                                                 
V 160    V   174                                                                 
F 161    L   175                                                                 
L 162    L   176                                                                 
M 163    F   177                                                                 
D 164    D   178                                                                 
E 165    E   179                                                                 
P 166    P   180                                                                 
L 167    T   181                                                                 
S 168    S   182                                                                 
N 169    A   183                                                                 
L 170    L   184                                                                 
D 171    D   185                                                                 
A 172    P   186                                                                 
K 173    E   187                                                                 
L 174    L   188                                                                 
R 175    V   189                                                                 
V 176    G   190                                                                 
R 177    E   191                                                                 
M 178    V   192                                                                 
R 179    L   193                                                                 
A 180    R   194                                                                 
E 181    I   195                                                                 
L 182    M   196                                                                 
K 183    Q   197                                                                 
K 184    Q   198                                                                 
L 185    L   199                                                                 
Q 186    A   200                                                                 
R 187    E   201                                                                 
Q 188    E   202                                                                 
G 190    G   203                                                                 
V 191    K   204                                                                 
T 192    T   205                                                                 
T 193    M   206                                                                 
I 194    V   207                                                                 
Y 195    V   208                                                                 
V 196    V   209                                                                 
T 197    T   210                                                                 
H 198    H   211                                                                 
D 199    E   212                                                                 
Q 200    M   213                                                                 
V 201    G   214                                                                 
E 202    F   215                                                                 
A 203    A   216                                                                 
M 204    R   217                                                                 
T 205    H   218                                                                 
M 206    V   219                                                                 
G 207    S   220                                                                 
D 208    S   221                                                                 
R 209    H   222                                                                 
I 210    V   223                                                                 
A 211    I   224                                                                 
V 212    F   225                                                                 
M 213    L   226                                                                 
N 214    H   227                                                                 
R 215    Q   228                                                                 
G 216    G   229                                                                 
V 217    K   230                                                                 
L 218    I   231                                                                 
Q 219    E   232                                                                 
Q 220    E   233                                                                 
V 221    E   234                                                                 
G 222    G   235                                                                 
S 223    D   236                                                                 
P 224    P   237                                                                 
D 225    E   238                                                                 
E 226    Q   239                                                                 
V 227    V   240                                                                 
Y 228    F   241                                                                 
D 229    G   242                                                                 
K 230    N   243                                                                 
P 231    P   244                                                                 
A 232    Q   245                                                                 
N 233    S   246                                                                 
T 234    P   247                                                                 
F 235    R   248                                                                 
V 236    L   249                                                                 
A 237    Q   250                                                                 
G 238    Q   251                                                                 
F 239    F   252                                                                 
I 240    L   253                                                                 
G 241    K   254                                                                 
S 242    G   255                                                                 
P 243    S   256                                                                 
P 244    L   257                                                                 
M 245    K   258                                                                 
N 246    K   259                                                                 
F 247    L   260                                                                 
L 248    E   261                                                                 
D 249    H   262                                                                 
TER                                                                              
END                                                                              



