
PFRMAT AL                                                                        
TARGET T0101                                                                     
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  4                                                                         
PARENT 1B2P_A                                                                    
G  92    N     1                                                                 
N  93    N     2                                                                 
T  94    I     3                                                                 
I  95    I     4                                                                 
T  96    F     5                                                                 
F  97    S     6                                                                 
N  98    K     7                                                                 
K  99    Q     8                                                                 
S 100    P     9                                                                 
G 101    D    10                                                                 
K 102    D    11                                                                 
D 103    N    12                                                                 
G 104    H    13                                                                 
A 105    P    14                                                                 
P 106    Q    15                                                                 
I 107    I    16                                                                 
Y 108    L    17                                                                 
V 109    H    18                                                                 
A 110    A    19                                                                 
R 116    T    20                                                                 
A 117    E    21                                                                 
V 118    S    22                                                                 
F 119    L    23                                                                 
D 120    E    24                                                                 
F 121    I    25                                                                 
S 122    L    26                                                                 
F 123    F    27                                                                 
P 124    G    28                                                                 
D 125    T    29                                                                 
S 126    H    30                                                                 
Q 127    V    31                                                                 
Y 133    Y    32                                                                 
G 134    R    33                                                                 
F 135    F    34                                                                 
Y 136    I    35                                                                 
V 137    M    36                                                                 
T 138    Q    37                                                                 
G 139    T    38                                                                 
D 140    D    39                                                                 
Y 141    L    42                                                                 
W 142    V    43                                                                 
Y 143    L    44                                                                 
F 144    D    46                                                                 
K 145    N    47                                                                 
G 146    N    48                                                                 
V 147    N    49                                                                 
E 148    P    50                                                                 
V 149    I    51                                                                 
T 150    W    52                                                                 
R 151    A    53                                                                 
A 152    T    54                                                                 
G 153    N    55                                                                 
Y 154    T    56                                                                 
Q 155    G    62                                                                 
G 156    C    63                                                                 
A 157    R    64                                                                 
Y 158    A    65                                                                 
V 159    V    66                                                                 
I 160    L    67                                                                 
G 161    Q    68                                                                 
S 162    P    69                                                                 
H 163    D    70                                                                 
N 164    G    71                                                                 
T 165    V    72                                                                 
F 166    L    73                                                                 
E 167    V    74                                                                 
A 170    V    75                                                                 
F 171    I    76                                                                 
H 172    T    77                                                                 
H 173    N    78                                                                 
N 174    E    79                                                                 
R 175    N    80                                                                 
N 176    V    81                                                                 
T 177    T    82                                                                 
G 178    V    83                                                                 
L 179    W    84                                                                 
E 180    Q    85                                                                 
I 181    S    86                                                                 
N 182    P    87                                                                 
N 183    V    88                                                                 
G 184    A    89                                                                 
G 185    G    90                                                                 
S 186    K    91                                                                 
Y 187    A    92                                                                 
N 188    G    93                                                                 
T 189    H    94                                                                 
V 190    Y    95                                                                 
Y 196    V    96                                                                 
R 197    L    97                                                                 
N 198    V    98                                                                 
Y 199    L    99                                                                 
D 200    Q   100                                                                 
P 201    P   101                                                                 
K 202    D   102                                                                 
K 203    R   103                                                                 
N 204    N   104                                                                 
G 205    V   105                                                                 
S 206    V   106                                                                 
M 207    I   107                                                                 
F 211    Y   108                                                                 
G 212    G   109                                                                 
P 213    D   110                                                                 
K 214    A   111                                                                 
Q 215    L   112                                                                 
K 216    W   113                                                                 
Q 217    A   114                                                                 
G 218    T   115                                                                 
P 219    Q   116                                                                 
G 220    T   117                                                                 
N 221    V   118                                                                 
R 222    R   119                                                                 
TER                                                                              
END                                                                              



