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



