
PFRMAT AL                                                                        
TARGET T0122                                                                     
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 1A5S_A                                                                    
M   1    L    11                                                                 
F   2    N    12                                                                 
K   3    R    15                                                                 
D   4    E    16                                                                 
G   5    G    17                                                                 
S   6    A    18                                                                 
L   7    F    19                                                                 
I   8    V    20                                                                 
P   9    P    21                                                                 
Y  10    F    22                                                                 
L  11    V    23                                                                 
T  12    T    24                                                                 
A  13    L    25                                                                 
G  14    G    26                                                                 
D  15    D    27                                                                 
P  16    P    28                                                                 
D  17    G    29                                                                 
K  18    I    30                                                                 
Q  19    E    31                                                                 
S  20    Q    32                                                                 
T  21    S    33                                                                 
L  22    L    34                                                                 
N  23    K    35                                                                 
F  24    I    36                                                                 
L  25    I    37                                                                 
L  26    D    38                                                                 
A  27    T    39                                                                 
L  28    L    40                                                                 
D  29    I    41                                                                 
E  30    A    43                                                                 
Y  31    G    44                                                                 
A  32    A    45                                                                 
G  33    D    46                                                                 
A  34    A    47                                                                 
I  35    L    48                                                                 
E  36    E    49                                                                 
L  37    L    50                                                                 
G  38    G    51                                                                 
I  39    V    52                                                                 
P  40    P    53                                                                 
F  41    F    54                                                                 
S  42    S    55                                                                 
D  43    D    56                                                                 
P  44    P    57                                                                 
I  45    L    58                                                                 
A  46    A    59                                                                 
D  47    D    60                                                                 
G  48    G    61                                                                 
K  49    P    62                                                                 
T  50    T    63                                                                 
I  51    I    64                                                                 
Q  52    Q    65                                                                 
E  53    N    66                                                                 
S  54    A    67                                                                 
H  55    N    68                                                                 
Y  56    L    69                                                                 
R  57    R    70                                                                 
A  58    A    71                                                                 
L  59    F    72                                                                 
K  60    A    73                                                                 
N  61    A    74                                                                 
G  62    G    75                                                                 
F  63    V    76                                                                 
K  64    T    77                                                                 
L  65    P    78                                                                 
R  66    A    79                                                                 
E  67    Q    80                                                                 
A  68    C    81                                                                 
F  69    F    82                                                                 
W  70    E    83                                                                 
I  71    M    84                                                                 
V  72    L    85                                                                 
K  73    A    86                                                                 
E  74    L    87                                                                 
F  75    I    88                                                                 
R  76    E    90                                                                 
R  77    K    91                                                                 
H  78    H    92                                                                 
S  79    P    93                                                                 
S  80    T    94                                                                 
T  81    I    95                                                                 
P  82    P    96                                                                 
I  83    I    97                                                                 
V  84    G    98                                                                 
L  85    L    99                                                                 
M  86    L   100                                                                 
T  87    M   101                                                                 
Y  88    Y   102                                                                 
Y  89    A   103                                                                 
N  90    N   104                                                                 
P  91    L   105                                                                 
I  92    V   106                                                                 
Y  93    F   107                                                                 
R  94    N   108                                                                 
A  95    N   109                                                                 
G  96    G   110                                                                 
V  97    I   111                                                                 
R  98    D   112                                                                 
N  99    A   113                                                                 
F 100    F   114                                                                 
L 101    Y   115                                                                 
A 102    A   116                                                                 
E 103    R   117                                                                 
A 104    C   118                                                                 
K 105    E   119                                                                 
A 106    Q   120                                                                 
S 107    V   121                                                                 
G 108    G   122                                                                 
V 109    V   123                                                                 
D 110    D   124                                                                 
G 111    S   125                                                                 
I 112    V   126                                                                 
L 113    L   127                                                                 
V 114    V   128                                                                 
V 115    A   129                                                                 
D 116    D   130                                                                 
L 117    V   131                                                                 
P 118    P   132                                                                 
V 119    V   133                                                                 
F 120    E   134                                                                 
H 121    E   135                                                                 
A 122    S   136                                                                 
K 123    A   137                                                                 
E 124    P   138                                                                 
F 125    F   139                                                                 
T 126    R   140                                                                 
E 127    Q   141                                                                 
I 128    A   142                                                                 
A 129    A   143                                                                 
R 130    L   144                                                                 
E 131    R   145                                                                 
E 132    H   146                                                                 
G 133    N   147                                                                 
I 134    I   148                                                                 
K 135    A   149                                                                 
T 136    P   150                                                                 
V 137    I   151                                                                 
F 138    F   152                                                                 
L 139    I   153                                                                 
A 140    C   154                                                                 
A 141    P   155                                                                 
P 142    P   156                                                                 
N 143    N   157                                                                 
T 144    A   158                                                                 
P 145    D   159                                                                 
D 146    D   160                                                                 
E 147    D   161                                                                 
R 148    L   162                                                                 
L 149    L   163                                                                 
K 150    R   164                                                                 
V 151    Q   165                                                                 
I 152    V   166                                                                 
D 153    A   167                                                                 
D 154    S   168                                                                 
M 155    Y   169                                                                 
T 156    G   170                                                                 
T 157    R   171                                                                 
G 158    G   172                                                                 
F 159    Y   173                                                                 
V 160    T   174                                                                 
Y 161    Y   175                                                                 
L 162    L   176                                                                 
V 163    L   177                                                                 
S 164    S   178                                                                 
L 165    R   179                                                                 
Y 166    S   180                                                                 
G 167    G   181                                                                 
T 168    V   182                                                                 
T 169    T   183                                                                 
G 170    G   184                                                                 
A 171    A   185                                                                 
R 172    E   186                                                                 
E 173    N   187                                                                 
K 177    L   196                                                                 
L 183    I   197                                                                 
R 184    E   198                                                                 
R 185    K   199                                                                 
A 186    L   200                                                                 
K 187    K   201                                                                 
R 188    E   202                                                                 
I 189    Y   203                                                                 
C 190    H   204                                                                 
R 191    A   205                                                                 
N 192    A   206                                                                 
K 193    P   207                                                                 
V 194    A   208                                                                 
A 195    L   209                                                                 
V 196    Q   210                                                                 
G 197    G   211                                                                 
F 198    F   212                                                                 
G 199    G   213                                                                 
V 200    I   214                                                                 
S 201    S   215                                                                 
K 202    S   216                                                                 
R 203    P   217                                                                 
E 204    E   218                                                                 
H 205    Q   219                                                                 
V 206    V   220                                                                 
V 207    S   221                                                                 
S 208    A   222                                                                 
L 209    A   223                                                                 
L 210    V   224                                                                 
K 211    R   225                                                                 
E 212    A   226                                                                 
G 213    G   227                                                                 
A 214    A   228                                                                 
N 215    A   229                                                                 
G 216    G   230                                                                 
V 217    A   231                                                                 
V 218    I   232                                                                 
V 219    S   233                                                                 
G 220    G   234                                                                 
S 221    S   235                                                                 
A 222    A   236                                                                 
L 223    I   237                                                                 
V 224    V   238                                                                 
K 225    K   239                                                                 
I 226    I   240                                                                 
I 227    I   241                                                                 
G 228    E   242                                                                 
E 229    K   243                                                                 
K 230    N   244                                                                 
G 231    L   245                                                                 
R 232    A   246                                                                 
E 233    S   247                                                                 
A 234    P   248                                                                 
T 235    K   249                                                                 
E 236    Q   250                                                                 
F 237    M   251                                                                 
L 238    L   252                                                                 
K 239    A   253                                                                 
K 241    E   254                                                                 
V 242    L   255                                                                 
E 243    R   256                                                                 
E 244    S   257                                                                 
L 245    F   258                                                                 
L 246    V   259                                                                 
G 247    S   260                                                                 
I 248    A   261                                                                 
TER                                                                              
END                                                                              



