
PFRMAT AL                                                                        
TARGET T0119                                                                     
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 1FRR_B                                                                    
N   3    A     1                                                                 
H   4    Y     2                                                                 
Q   5    K     3                                                                 
V   6    T     4                                                                 
A   7    V     5                                                                 
L   8    L     6                                                                 
Q   9    K     7                                                                 
F  10    T     8                                                                 
E  11    P     9                                                                 
D  12    S    10                                                                 
G  13    G    11                                                                 
V  14    E    12                                                                 
T  15    F    13                                                                 
R  16    T    14                                                                 
F  17    L    15                                                                 
I  18    D    16                                                                 
I  20    V    17                                                                 
A  21    P    18                                                                 
Q  22    E    19                                                                 
G  23    G    20                                                                 
E  24    T    21                                                                 
T  25    T    22                                                                 
L  26    I    23                                                                 
S  27    L    24                                                                 
D  28    D    25                                                                 
A  29    A    26                                                                 
A  30    A    27                                                                 
Y  31    E    28                                                                 
R  32    E    29                                                                 
Q  33    A    30                                                                 
Q  34    G    31                                                                 
I  35    Y    32                                                                 
N  36    D    33                                                                 
I  37    L    34                                                                 
P  38    P    35                                                                 
M  39    F    36                                                                 
D  40    S    37                                                                 
C  41    C    38                                                                 
R  42    R    39                                                                 
E  43    A    40                                                                 
G  44    G    41                                                                 
E  45    A    42                                                                 
C  46    C    43                                                                 
G  47    S    44                                                                 
T  48    S    45                                                                 
C  49    C    46                                                                 
R  50    L    47                                                                 
A  51    G    48                                                                 
F  52    K    49                                                                 
C  53    V    50                                                                 
E  54    V    51                                                                 
S  55    S    52                                                                 
G  56    G    53                                                                 
N  57    S    54                                                                 
Y  58    V    55                                                                 
D  59    D    56                                                                 
M  60    E    57                                                                 
P  61    S    58                                                                 
E  62    E    59                                                                 
D  63    G    60                                                                 
N  64    S    61                                                                 
Y  65    F    62                                                                 
I  66    L    63                                                                 
E  67    D    64                                                                 
D  68    D    65                                                                 
E  73    G    66                                                                 
E  74    Q    67                                                                 
A  75    M    68                                                                 
Q  76    E    69                                                                 
Q  77    E    70                                                                 
G  78    G    71                                                                 
Y  79    F    72                                                                 
V  80    V    73                                                                 
L  81    L    74                                                                 
A  82    T    75                                                                 
C  83    C    76                                                                 
Q  84    I    77                                                                 
C  85    A    78                                                                 
R  86    I    79                                                                 
P  87    P    80                                                                 
T  88    E    81                                                                 
S  89    S    82                                                                 
D  90    D    83                                                                 
A  91    L    84                                                                 
V  92    V    85                                                                 
F  93    I    86                                                                 
Q  94    E    87                                                                 
I  95    T    88                                                                 
Q  96    H    89                                                                 
A  97    K    90                                                                 
S  98    E    91                                                                 
I 106    E    92                                                                 
H 107    E    93                                                                 
H 108    L    94                                                                 
F 109    F    95                                                                 
TER                                                                              
END                                                                              



