
PFRMAT AL                                                                        
TARGET T0114                                                                     
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 1BQS_A                                                                    
I   2    V     1                                                                 
N   3    K     2                                                                 
R   4    P     3                                                                 
T   5    L     4                                                                 
D   6    Q     5                                                                 
C   7    V     6                                                                 
N   8    E     7                                                                 
E   9    P     8                                                                 
N  10    P     9                                                                 
S  11    P    11                                                                 
Y  12    V    12                                                                 
L  13    V    13                                                                 
E  14    A    14                                                                 
I  15    V    15                                                                 
H  16    A    16                                                                 
N  17    L    17                                                                 
N  18    G    18                                                                 
E  19    A    19                                                                 
G  20    S    20                                                                 
R  21    R    21                                                                 
D  22    Q    22                                                                 
T  23    L    23                                                                 
L  24    T    24                                                                 
C  25    C    25                                                                 
F  26    R    26                                                                 
A  27    L    27                                                                 
N  28    A    28                                                                 
A  29    C    29                                                                 
G  30    A    30                                                                 
T  31    D    31                                                                 
M  32    R    32                                                                 
P  33    G    33                                                                 
V  34    A    34                                                                 
G  38    S    35                                                                 
V  39    V    36                                                                 
N  40    Q    37                                                                 
W  41    W    38                                                                 
V  42    R    39                                                                 
E  43    G    40                                                                 
S  44    L    41                                                                 
G  45    D    42                                                                 
N  46    T    43                                                                 
N  47    S    44                                                                 
V  48    L    45                                                                 
V  49    G    46                                                                 
T  50    A    47                                                                 
L  51    V    48                                                                 
Q  52    Q    49                                                                 
F  53    S    50                                                                 
Q  54    D    51                                                                 
R  55    R    54                                                                 
N  56    S    55                                                                 
L  57    V    56                                                                 
S  58    L    57                                                                 
D  59    T    58                                                                 
P  60    V    59                                                                 
R  61    R    60                                                                 
L  62    N    61                                                                 
E  63    A    62                                                                 
T  64    R    70                                                                 
I  65    V    71                                                                 
T  66    C    72                                                                 
L  67    V    73                                                                 
Q  68    G    74                                                                 
K  69    S    75                                                                 
W  70    C    76                                                                 
N  74    G    77                                                                 
P  75    G    78                                                                 
G  76    R    79                                                                 
H  77    T    80                                                                 
I  78    F    81                                                                 
H  79    Q    82                                                                 
E  80    H    83                                                                 
I  81    T    84                                                                 
L  82    V    85                                                                 
S  83    Q    86                                                                 
I  84    L    87                                                                 
R  85    L    88                                                                 
I  86    V    89                                                                 
Y  87    Y    90                                                                 
TER                                                                              
END                                                                              



