
PFRMAT AL                                                                        
TARGET T0108                                                                     
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 1NTD                                                                      
P  23    T     5                                                                 
V  24    A     6                                                                 
T  25    A     7                                                                 
N  26    E     8                                                                 
Q  27    I     9                                                                 
P  28    A    10                                                                 
T  29    A    11                                                                 
A  30    L    12                                                                 
P  31    P    13                                                                 
K  32    R    14                                                                 
D  33    Q    15                                                                 
F  34    K    16                                                                 
S  35    V    17                                                                 
G  37    E    18                                                                 
F  38    L    19                                                                 
W  39    V    20                                                                 
D  40    D    21                                                                 
F  41    P    22                                                                 
N  42    P    23                                                                 
D  43    F    24                                                                 
G  44    V    25                                                                 
T  45    H    26                                                                 
T  46    A    27                                                                 
Q  47    H    28                                                                 
G  48    S    29                                                                 
F  49    Q    30                                                                 
G  50    V    31                                                                 
V  51    A    32                                                                 
N  52    E    33                                                                 
P  53    G    34                                                                 
D  54    G    35                                                                 
S  55    P    36                                                                 
P  56    K    37                                                                 
I  57    V    38                                                                 
T  58    V    39                                                                 
A  59    E    40                                                                 
I  60    F    41                                                                 
N  61    T    42                                                                 
V  62    M    43                                                                 
E  63    V    44                                                                 
L  69    I    45                                                                 
K  70    E    46                                                                 
I  71    E    47                                                                 
S  72    K    48                                                                 
N  73    K    49                                                                 
L  74    I    50                                                                 
N  75    V    51                                                                 
S  76    I    52                                                                 
K  77    D    53                                                                 
G  78    D    54                                                                 
S  79    A    55                                                                 
N  80    G    56                                                                 
D  81    T    57                                                                 
F  87    E    58                                                                 
W  88    V    59                                                                 
A  89    H    60                                                                 
N  90    A    61                                                                 
V  91    M    62                                                                 
R  92    A    63                                                                 
I  93    F    64                                                                 
S  94    N    65                                                                 
A  95    G    66                                                                 
D  96    T    67                                                                 
I  97    V    68                                                                 
W  98    P    69                                                                 
G  99    G    70                                                                 
Q 100    P    71                                                                 
S 101    L    72                                                                 
I 102    M    73                                                                 
N 103    V    74                                                                 
I 104    V    75                                                                 
Y 105    H    76                                                                 
G 106    Q    77                                                                 
D 107    D    78                                                                 
T 108    D    79                                                                 
K 109    Y    80                                                                 
L 110    L    81                                                                 
T 111    E    82                                                                 
M 112    L    83                                                                 
D 113    T    84                                                                 
V 114    L    85                                                                 
I 115    I    86                                                                 
A 116    N    87                                                                 
P 117    P    88                                                                 
T 118    L    93                                                                 
P 119    M    94                                                                 
V 120    H    95                                                                 
N 121    N    96                                                                 
V 122    I    97                                                                 
S 123    D    98                                                                 
I 124    F    99                                                                 
A 125    H   100                                                                 
A 126    A   101                                                                 
I 127    A   102                                                                 
P 128    G   107                                                                 
Q 129    G   108                                                                 
S 130    G   109                                                                 
S 131    G   110                                                                 
T 132    L   111                                                                 
H 133    T   112                                                                 
G 134    E   113                                                                 
W 135    I   114                                                                 
G 136    N   115                                                                 
N 137    P   116                                                                 
P 138    G   117                                                                 
T 139    E   118                                                                 
R 140    K   119                                                                 
A 141    T   120                                                                 
R 142    I   121                                                                 
I 143    L   122                                                                 
V 144    R   123                                                                 
W 145    F   124                                                                 
T 146    K   125                                                                 
Q 152    A   126                                                                 
T 153    T   127                                                                 
D 154    K   128                                                                 
G 155    P   129                                                                 
T 156    G   130                                                                 
Y 157    V   131                                                                 
K 158    F   132                                                                 
T 162    V   133                                                                 
I 163    Y   134                                                                 
S 164    H   135                                                                 
T 165    C   136                                                                 
N 166    A   137                                                                 
D 167    P   138                                                                 
S 168    P   139                                                                 
P 169    G   140                                                                 
N 170    M   141                                                                 
F 171    V   142                                                                 
N 172    P   143                                                                 
T 173    W   144                                                                 
I 174    H   145                                                                 
A 175    V   146                                                                 
T 176    V   147                                                                 
D 177    S   148                                                                 
T 184    G   149                                                                 
N 185    E   150                                                                 
M 186    N   151                                                                 
I 187    G   152                                                                 
L 188    A   153                                                                 
F 189    I   154                                                                 
V 190    M   155                                                                 
G 191    V   156                                                                 
S 192    L   157                                                                 
N 193    P   158                                                                 
S 194    R   159                                                                 
D 195    E   160                                                                 
N 196    G   161                                                                 
I 197    L   162                                                                 
S 198    H   163                                                                 
L 199    D   164                                                                 
D 200    G   165                                                                 
N 201    K   166                                                                 
TER                                                                              
END                                                                              



