
PFRMAT AL                                                                        
TARGET T0126                                                                     
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 1C9K_C                                                                    
L  27    M     1                                                                 
R  28    I     2                                                                 
V  29    L     3                                                                 
E  30    V     4                                                                 
S  31    T     5                                                                 
L  32    G     6                                                                 
K  33    G     7                                                                 
Q  34    A     8                                                                 
R  35    R     9                                                                 
G  36    S    10                                                                 
E  37    G    11                                                                 
K  38    K    12                                                                 
K  39    S    13                                                                 
Q  40    R    14                                                                 
D  41    H    15                                                                 
G  42    A    16                                                                 
E  43    E    17                                                                 
K  44    A    18                                                                 
L  45    L    19                                                                 
I  46    I    20                                                                 
R  47    G    21                                                                 
P  48    D    22                                                                 
A  49    A    23                                                                 
E  50    P    24                                                                 
S  51    Q    25                                                                 
V  52    V    26                                                                 
Y  53    L    27                                                                 
R  54    Y    28                                                                 
L  55    I    29                                                                 
D  56    A    30                                                                 
Q  60    H    45                                                                 
Q  61    H    46                                                                 
K  62    K    47                                                                 
L  63    D    48                                                                 
Q  64    R    50                                                                 
F  65    P    51                                                                 
D  66    A    52                                                                 
H  67    H    53                                                                 
W  68    W    54                                                                 
N  69    R    55                                                                 
V  70    T    56                                                                 
S  84    A    57                                                                 
T  88    R    61                                                                 
P  89    H    62                                                                 
D  90    L    63                                                                 
T  92    D    64                                                                 
N  93    T    65                                                                 
L  94    L    66                                                                 
M  95    I    67                                                                 
T  96    T    68                                                                 
R  97    A    69                                                                 
Q  98    D    70                                                                 
L  99    L    71                                                                 
L 100    A    72                                                                 
D 101    P    73                                                                 
P 102    D    74                                                                 
A 103    D    75                                                                 
A 104    A    76                                                                 
I 105    I    77                                                                 
F 106    L    78                                                                 
W 107    L    79                                                                 
R 108    E    80                                                                 
K 109    C    81                                                                 
D 113    D    98                                                                 
A 114    P    99                                                                 
M 115    E   100                                                                 
D 116    Q   101                                                                 
W 117    W   102                                                                 
N 118    D   103                                                                 
E 119    Y   104                                                                 
A 120    A   105                                                                 
D 121    A   106                                                                 
A 122    E   108                                                                 
L 123    R   109                                                                 
E 124    A   110                                                                 
F 125    I   111                                                                 
G 126    D   112                                                                 
E 127    D   113                                                                 
R 128    E   114                                                                 
L 129    I   115                                                                 
S 130    Q   116                                                                 
D 131    I   117                                                                 
L 132    L   118                                                                 
A 133    I   119                                                                 
K 134    A   120                                                                 
I 135    A   121                                                                 
R 136    A   127                                                                 
K 137    K   128                                                                 
V 138    V   129                                                                 
M 139    V   130                                                                 
Y 140    L   131                                                                 
F 141    V   132                                                                 
L 142    T   133                                                                 
I 143    N   134                                                                 
T 144    E   135                                                                 
F 145    V   136                                                                 
G 146    G   137                                                                 
E 147    M   138                                                                 
G 148    G   139                                                                 
V 149    I   140                                                                 
E 150    V   141                                                                 
P 151    P   142                                                                 
A 152    E   143                                                                 
N 153    N   144                                                                 
L 154    R   145                                                                 
K 155    L   146                                                                 
S 157    A   147                                                                 
V 158    R   148                                                                 
V 159    H   149                                                                 
F 160    F   150                                                                 
N 161    R   151                                                                 
Q 162    D   152                                                                 
L 163    I   153                                                                 
TER                                                                              
END                                                                              



