
PFRMAT AL                                                                        
TARGET T0117                                                                     
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 1TPB_1                                                                    
M   1    L    21                                                                 
A   2    G    22                                                                 
E   3    E    23                                                                 
A   4    L    24                                                                 
A   5    I    25                                                                 
S   6    H    26                                                                 
C   7    T    27                                                                 
A   8    L    28                                                                 
K  10    N    29                                                                 
G  11    G    30                                                                 
T  12    A    31                                                                 
K  13    K    32                                                                 
Y  14    L    33                                                                 
A  15    S    34                                                                 
E  16    A    35                                                                 
G  17    D    36                                                                 
T  18    T    37                                                                 
Q  19    E    38                                                                 
P  20    V    39                                                                 
F  21    V    40                                                                 
T  22    C    41                                                                 
V  23    G    42                                                                 
G  32    A    43                                                                 
K  33    P    44                                                                 
T  34    S    45                                                                 
T  35    I    46                                                                 
Y  36    Y    47                                                                 
L  37    L    48                                                                 
N  38    D    49                                                                 
H  39    F    50                                                                 
F  40    A    51                                                                 
E  41    Q    53                                                                 
K  42    K    54                                                                 
Y  43    L    55                                                                 
K  44    D    56                                                                 
N  45    A    57                                                                 
D  46    K    58                                                                 
I  47    I    59                                                                 
C  48    G    60                                                                 
L  49    V    61                                                                 
L  50    A    62                                                                 
T  51    A    63                                                                 
E  67    Q    64                                                                 
L  68    N    65                                                                 
M  69    C    66                                                                 
Y  70    Y    67                                                                 
K  71    K    68                                                                 
D  72    V    69                                                                 
P  73    P    70                                                                 
K  74    K    71                                                                 
K  75    G    72                                                                 
W  76    A    73                                                                 
F  80    F    74                                                                 
Q  81    T    75                                                                 
S  82    G    76                                                                 
Y  83    E    77                                                                 
V  84    I    78                                                                 
T  85    S    79                                                                 
L  86    P    80                                                                 
T  87    A    81                                                                 
M  88    M    82                                                                 
L  89    I    83                                                                 
Q  90    K    84                                                                 
S  91    D    85                                                                 
H  92    H   100                                                                 
T  93    V   101                                                                 
A  94    F   102                                                                 
P  95    G   103                                                                 
T  96    E   104                                                                 
N  97    S   105                                                                 
K  98    D   106                                                                 
K  99    E   107                                                                 
L 100    L   108                                                                 
K 101    I   109                                                                 
I 102    K   112                                                                 
M 103    V   113                                                                 
E 104    A   114                                                                 
R 105    H   115                                                                 
S 106    A   116                                                                 
I 107    L   117                                                                 
F 108    L   121                                                                 
S 109    G   122                                                                 
A 110    V   123                                                                 
R 111    I   124                                                                 
Y 112    A   125                                                                 
C 113    C   126                                                                 
F 114    I   127                                                                 
V 115    G   128                                                                 
E 116    E   129                                                                 
N 117    K   130                                                                 
M 118    L   131                                                                 
R 119    R   134                                                                 
R 120    E   135                                                                 
N 121    A   136                                                                 
G 122    G   137                                                                 
S 123    I   138                                                                 
L 124    T   139                                                                 
E 125    E   140                                                                 
Q 126    K   141                                                                 
G 127    V   142                                                                 
M 128    V   143                                                                 
Y 129    F   144                                                                 
N 130    E   145                                                                 
T 131    Q   146                                                                 
L 132    T   147                                                                 
K 137    K   148                                                                 
F 138    A   149                                                                 
I 139    I   150                                                                 
E 140    A   151                                                                 
E 141    D   152                                                                 
S 142    N   153                                                                 
I 143    V   154                                                                 
H 144    K   155                                                                 
V 145    D   156                                                                 
Q 146    W   157                                                                 
A 147    S   158                                                                 
D 148    K   159                                                                 
L 149    V   160                                                                 
I 150    V   161                                                                 
I 151    L   162                                                                 
Y 152    A   163                                                                 
Y 161    Y   164                                                                 
E 162    D   165                                                                 
R 163    P   166                                                                 
I 164    V   167                                                                 
R 165    W   168                                                                 
A 168    A   169                                                                 
R 169    I   170                                                                 
S 170    G   171                                                                 
E 171    T   172                                                                 
E 172    G   173                                                                 
S 173    K   174                                                                 
C 174    T   175                                                                 
V 175    A   176                                                                 
P 176    T   177                                                                 
L 177    P   178                                                                 
K 178    Q   179                                                                 
Y 179    Q   180                                                                 
L 180    A   181                                                                 
Q 181    Q   182                                                                 
E 182    E   183                                                                 
L 183    V   184                                                                 
H 184    H   185                                                                 
E 185    E   186                                                                 
L 186    K   187                                                                 
H 187    L   188                                                                 
E 188    R   189                                                                 
D 189    G   190                                                                 
W 190    W   191                                                                 
L 191    L   192                                                                 
I 192    K   193                                                                 
H 193    T   194                                                                 
Q 194    D   198                                                                 
R 195    A   199                                                                 
R 196    V   200                                                                 
P 197    A   201                                                                 
Q 198    Q   202                                                                 
S 199    S   203                                                                 
C 200    T   204                                                                 
K 201    R   205                                                                 
V 202    I   206                                                                 
L 203    I   207                                                                 
V 204    Y   208                                                                 
L 205    G   209                                                                 
D 206    G   210                                                                 
A 207    S   211                                                                 
S 221    V   212                                                                 
E 222    T   213                                                                 
S 223    G   214                                                                 
S 224    G   215                                                                 
I 225    N   216                                                                 
F 226    C   217                                                                 
D 227    K   218                                                                 
A 228    E   219                                                                 
I 229    L   220                                                                 
S 230    A   221                                                                 
S 231    S   222                                                                 
N 232    Q   223                                                                 
Q 233    H   224                                                                 
Q 234    D   225                                                                 
P 235    V   226                                                                 
S 236    D   227                                                                 
P 237    G   228                                                                 
V 238    F   229                                                                 
L 239    L   230                                                                 
V 240    V   231                                                                 
S 241    G   232                                                                 
P 242    G   233                                                                 
S 243    A   234                                                                 
K 244    S   235                                                                 
R 245    P   238                                                                 
Q 246    E   239                                                                 
R 247    F   240                                                                 
V 248    V   241                                                                 
A 249    D   242                                                                 
R 250    H   248                                                                 
TER                                                                              
END                                                                              



