
PFRMAT AL                                                                        
TARGET T0120                                                                     
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 1CKE_A                                                                    
M   1    M    25                                                                 
E   2    A    26                                                                 
R   3    E    27                                                                 
K   4    A    28                                                                 
I   5    L    29                                                                 
R   7    Q    30                                                                 
I   8    W    31                                                                 
H   9    H    32                                                                 
L  10    L    33                                                                 
V  11    L    34                                                                 
S  12    D    35                                                                 
E  13    S    36                                                                 
P  14    G    37                                                                 
S  15    A    38                                                                 
I  16    I    39                                                                 
T  17    Y    40                                                                 
H  18    R    41                                                                 
F  19    V    42                                                                 
L  20    L    43                                                                 
Q  21    A    44                                                                 
V  22    V    54                                                                 
S  23    A    55                                                                 
W  24    S    56                                                                 
E  25    E    57                                                                 
K  26    D    58                                                                 
T  27    A    59                                                                 
L  28    L    60                                                                 
E  29    A    64                                                                 
S  30    S    65                                                                 
G  31    H    66                                                                 
F  32    L    67                                                                 
V  33    D    68                                                                 
I  34    V    69                                                                 
T  35    R    70                                                                 
L  36    F    71                                                                 
T  37    V    72                                                                 
D  38    S    73                                                                 
G  39    T    74                                                                 
H  40    N    75                                                                 
S  41    G    76                                                                 
A  42    N    77                                                                 
W  43    L    78                                                                 
T  44    E    79                                                                 
G  45    V    80                                                                 
T  46    I    81                                                                 
V  47    L    82                                                                 
S  48    E    83                                                                 
E  49    G    84                                                                 
S  50    E    85                                                                 
E  51    D    86                                                                 
I  52    V    87                                                                 
S  53    S    88                                                                 
Q  54    G    89                                                                 
E  55    E    90                                                                 
A  56    I    91                                                                 
D  57    R    92                                                                 
D  58    T    93                                                                 
M  59    Q    94                                                                 
A  60    E    95                                                                 
M  61    V    96                                                                 
E  62    A    97                                                                 
K  63    N    98                                                                 
G  64    A   100                                                                 
K  65    S   101                                                                 
Y  66    Q   102                                                                 
V  67    V   103                                                                 
G  68    A   104                                                                 
E  69    A   105                                                                 
L  70    F   106                                                                 
R  71    R   110                                                                 
K  72    E   111                                                                 
A  73    A   112                                                                 
L  74    L   113                                                                 
L  75    L   114                                                                 
S  76    R   115                                                                 
G  77    R   116                                                                 
T  85    Q   117                                                                 
F  86    R   118                                                                 
N  87    A   119                                                                 
F  88    F   120                                                                 
S  89    R   121                                                                 
K  90    E   122                                                                 
E  91    L   123                                                                 
S  92    P   124                                                                 
C  93    G   125                                                                 
Y  94    L   126                                                                 
F  95    I   127                                                                 
F  96    A   128                                                                 
F  97    D   129                                                                 
E  98    G   130                                                                 
K  99    R   131                                                                 
N 100    D   132                                                                 
L 101    M   133                                                                 
K 102    G   134                                                                 
D 103    T   135                                                                 
V 104    V   136                                                                 
S 105    V   137                                                                 
F 106    F   138                                                                 
R 107    P   139                                                                 
L 108    D   140                                                                 
G 109    A   141                                                                 
E 125    P   142                                                                 
L 126    V   143                                                                 
I 127    K   144                                                                 
C 128    I   145                                                                 
Y 129    F   146                                                                 
C 130    L   147                                                                 
L 131    D   148                                                                 
D 132    A   149                                                                 
T 133    S   150                                                                 
I 134    S   151                                                                 
A 135    E   152                                                                 
E 136    E   153                                                                 
N 137    R   154                                                                 
Q 138    A   155                                                                 
A 139    H   156                                                                 
K 140    R   158                                                                 
N 141    M   159                                                                 
E 142    L   160                                                                 
H 143    Q   161                                                                 
L 144    L   162                                                                 
Q 145    Q   163                                                                 
K 146    V   164                                                                 
E 147    N   170                                                                 
N 148    F   171                                                                 
E 149    E   172                                                                 
R 150    R   173                                                                 
L 151    L   174                                                                 
L 152    L   175                                                                 
R 153    A   176                                                                 
D 154    E   177                                                                 
W 155    I   178                                                                 
N 156    K   179                                                                 
C 165    T   206                                                                 
V 166    L   207                                                                 
S 167    S   208                                                                 
A 168    I   209                                                                 
K 169    E   210                                                                 
E 170    Q   211                                                                 
A 171    V   212                                                                 
L 172    I   213                                                                 
E 173    E   214                                                                 
T 174    K   215                                                                 
D 175    A   216                                                                 
L 176    Q   218                                                                 
Y 177    Y   219                                                                 
K 178    A   220                                                                 
R 179    R   221                                                                 
F 180    Q   222                                                                 
I 181    K   223                                                                 
L 182    L   224                                                                 
V 183    A   225                                                                 
L 184    L   226                                                                 
N 185    A   227                                                                 
TER                                                                              
END                                                                              



