
PFRMAT AL                                                                        
TARGET T0107                                                                     
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  3                                                                         
PARENT 1JLX_B                                                                    
V   1    C     8                                                                 
A   2    L     9                                                                 
T   3    K    10                                                                 
A   4    S    11                                                                 
K   5    N    12                                                                 
Y   6    N    13                                                                 
G   7    H    14                                                                 
T   8    Q    15                                                                 
P   9    K    16                                                                 
V  10    R    19                                                                 
I  11    Y    20                                                                 
D  12    Q    21                                                                 
G  13    S    22                                                                 
E  14    D    23                                                                 
I  15    Q    27                                                                 
D  16    Y    28                                                                 
E  17    G    29                                                                 
I  18    L    30                                                                 
W  19    L    31                                                                 
N  20    Q    32                                                                 
T  21    F    33                                                                 
A  31    S    34                                                                 
M  32    A    35                                                                 
G  33    D    36                                                                 
S  34    K    37                                                                 
L  35    I    38                                                                 
D  36    L    39                                                                 
K  37    D    40                                                                 
A  39    P    41                                                                 
T  40    L    42                                                                 
A  41    A    43                                                                 
K  42    Q    44                                                                 
V  43    F    45                                                                 
R  44    E    46                                                                 
V  45    V    47                                                                 
L  46    E    48                                                                 
W  47    P    49                                                                 
D  48    S    50                                                                 
E  49    D    54                                                                 
N  50    G    55                                                                 
Y  51    L    56                                                                 
L  52    V    57                                                                 
Y  53    H    58                                                                 
V  54    I    59                                                                 
L  55    K    60                                                                 
A  56    S    61                                                                 
I  57    R    62                                                                 
V  58    Y    63                                                                 
K  59    T    64                                                                 
D  60    N    65                                                                 
P  61    K    66                                                                 
V  62    Y    67                                                                 
L  63    L    68                                                                 
N  64    V    69                                                                 
K  65    W    71                                                                 
D  66    S    72                                                                 
N  67    P    73                                                                 
S  68    N    74                                                                 
N  69    H    75                                                                 
P  70    Y    76                                                                 
S  75    W    77                                                                 
V  76    I    78                                                                 
E  77    T    79                                                                 
I  78    A    80                                                                 
F  79    S    81                                                                 
I  80    A    82                                                                 
D  81    N    83                                                                 
E  82    E    84                                                                 
N  83    P    85                                                                 
N  84    D    86                                                                 
H  85    E    87                                                                 
K  86    N    88                                                                 
T  87    K    89                                                                 
G  88    S    90                                                                 
Y  89    N    91                                                                 
Y  90    W    92                                                                 
E  91    A    93                                                                 
D  94    C    94                                                                 
A  95    T    95                                                                 
Q  96    L    96                                                                 
F  97    F    97                                                                 
R  98    K    98                                                                 
V  99    P    99                                                                 
N 100    L   100                                                                 
Y 101    Y   101                                                                 
G 108    V   102                                                                 
T 109    E   103                                                                 
G 110    E   104                                                                 
G 111    G   105                                                                 
S 112    N   106                                                                 
P 113    M   107                                                                 
A 114    K   108                                                                 
R 115    K   109                                                                 
F 116    V   110                                                                 
K 117    R   111                                                                 
V 120    L   112                                                                 
K 121    L   113                                                                 
L 122    H   114                                                                 
I 123    V   115                                                                 
E 124    Q   116                                                                 
G 125    L   117                                                                 
G 126    G   118                                                                 
Y 127    H   119                                                                 
I 128    Y   120                                                                 
V 129    T   121                                                                 
E 130    Q   122                                                                 
K 134    N   123                                                                 
W 135    Y   124                                                                 
K 136    T   125                                                                 
T 137    V   126                                                                 
I 138    G   127                                                                 
K 139    G   128                                                                 
P 140    S   129                                                                 
T 141    F   130                                                                 
P 142    V   131                                                                 
N 143    S   132                                                                 
T 144    Y   133                                                                 
V 145    L   134                                                                 
I 146    F   135                                                                 
I 165    A   136                                                                 
S 166    E   137                                                                 
W 167    S   138                                                                 
S 168    S   139                                                                 
D 169    Q   140                                                                 
P 170    I   141                                                                 
T 171    D   142                                                                 
N 172    T   143                                                                 
S 179    G   144                                                                 
K 180    S   145                                                                 
F 181    K   146                                                                 
G 182    D   147                                                                 
N 183    V   148                                                                 
L 184    F   149                                                                 
R 185    H   150                                                                 
L 186    V   151                                                                 
I 187    I   152                                                                 
K 188    D   153                                                                 
TER                                                                              
END                                                                              



