
PFRMAT AL                                                                        
TARGET T0109                                                                     
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 3AKY                                                                      
D   4    E     3                                                                 
K   5    S     4                                                                 
Q   6    I     5                                                                 
N   7    R     6                                                                 
L   8    M     7                                                                 
I   9    V     8                                                                 
W  10    L     9                                                                 
I  11    I    10                                                                 
D  12    G    11                                                                 
L  13    P    12                                                                 
E  14    P    13                                                                 
M  15    G    14                                                                 
T  16    A    15                                                                 
G  17    G    16                                                                 
L  18    K    17                                                                 
D  19    G    18                                                                 
P  20    T    19                                                                 
E  21    Q    20                                                                 
K  22    A    21                                                                 
E  23    P    22                                                                 
R  24    N    23                                                                 
I  25    L    24                                                                 
I  26    Q    25                                                                 
E  27    E    26                                                                 
I  28    R    27                                                                 
A  29    F    28                                                                 
T  30    H    29                                                                 
I  31    H    32                                                                 
V  32    L    33                                                                 
T  33    A    34                                                                 
D  34    T    35                                                                 
K  35    G    36                                                                 
N  36    D    37                                                                 
L  37    L    39                                                                 
N  38    R    40                                                                 
I  39    S    41                                                                 
L  40    Q    42                                                                 
A  41    I    43                                                                 
E  42    A    44                                                                 
G  43    K    45                                                                 
P  44    G    46                                                                 
V  45    T    47                                                                 
L  46    Q    48                                                                 
A  47    L    49                                                                 
V  48    G    50                                                                 
H  49    L    51                                                                 
Q  50    E    52                                                                 
S  51    A    53                                                                 
D  52    K    54                                                                 
E  53    K    55                                                                 
L  54    I    56                                                                 
L  55    M    57                                                                 
N  56    D    58                                                                 
K  57    Q    59                                                                 
M  58    G    60                                                                 
N  59    G    61                                                                 
T  65    L    62                                                                 
H  66    V    63                                                                 
S  67    S    64                                                                 
E  68    D    65                                                                 
N  69    D    66                                                                 
G  70    I    67                                                                 
L  71    M    68                                                                 
I  72    V    69                                                                 
E  73    N    70                                                                 
R  74    M    71                                                                 
I  75    I    72                                                                 
K  76    K    73                                                                 
A  77    D    74                                                                 
S  78    E    75                                                                 
K  79    L    76                                                                 
L  80    T    77                                                                 
T  81    N    78                                                                 
E  82    N    79                                                                 
R  83    P    80                                                                 
A  84    A    81                                                                 
A  85    C    82                                                                 
E  86    K    83                                                                 
L  87    N    84                                                                 
Q  88    P    96                                                                 
T  89    Q    97                                                                 
L  90    A    98                                                                 
D  91    E    99                                                                 
F  92    K   100                                                                 
L  93    L   101                                                                 
K  94    D   102                                                                 
K  95    Q   103                                                                 
W  96    M   104                                                                 
V  97    K   106                                                                 
P  98    E   107                                                                 
K  99    Q   108                                                                 
G 100    G   109                                                                 
A 101    T   110                                                                 
S 102    P   111                                                                 
P 103    L   112                                                                 
R 114    E   113                                                                 
F 115    K   114                                                                 
L 116    A   115                                                                 
V 117    I   116                                                                 
K 118    E   117                                                                 
Y 119    L   118                                                                 
M 120    K   119                                                                 
P 121    V   120                                                                 
D 122    D   121                                                                 
L 123    D   122                                                                 
A 124    E   123                                                                 
D 125    L   124                                                                 
F 127    L   125                                                                 
H 128    V   126                                                                 
Y 129    A   127                                                                 
R 130    R   128                                                                 
H 131    I   129                                                                 
L 132    T   130                                                                 
D 133    N   169                                                                 
V 134    A   170                                                                 
S 135    D   171                                                                 
T 136    A   172                                                                 
L 137    L   173                                                                 
K 138    K   174                                                                 
E 139    K   175                                                                 
L 140    R   176                                                                 
A 141    L   177                                                                 
A 142    A   178                                                                 
R 143    A   182                                                                 
W 144    Q   183                                                                 
K 145    T   184                                                                 
P 146    E   185                                                                 
E 147    P   186                                                                 
I 148    I   187                                                                 
L 149    V   188                                                                 
E 150    D   189                                                                 
G 151    F   190                                                                 
F 152    Y   191                                                                 
K 153    K   192                                                                 
K 154    K   193                                                                 
E 155    T   194                                                                 
N 156    G   195                                                                 
T 157    I   196                                                                 
H 158    W   197                                                                 
L 159    A   198                                                                 
A 160    A   202                                                                 
L 161    S   203                                                                 
D 162    Q   204                                                                 
D 163    P   205                                                                 
I 164    P   206                                                                 
R 165    A   207                                                                 
E 166    T   208                                                                 
S 167    V   209                                                                 
I 168    W   210                                                                 
K 169    A   211                                                                 
E 170    D   212                                                                 
L 171    F   213                                                                 
A 172    L   214                                                                 
Y 173    N   215                                                                 
Y 174    K   216                                                                 
M 179    L   217                                                                 
K 180    G   218                                                                 
L 181    K   219                                                                 
D 182    N   220                                                                 
TER                                                                              
END                                                                              



