
PFRMAT AL                                                                        
TARGET T0102                                                                     
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 1BJY_A                                                                    
P   8    S     2                                                                 
A   9    R     3                                                                 
A  10    L     4                                                                 
V  11    N     5                                                                 
A  12    R     6                                                                 
G  13    E     7                                                                 
T  14    S     8                                                                 
V  15    V     9                                                                 
L  16    I    10                                                                 
N  17    D    11                                                                 
V  18    A    12                                                                 
V  19    A    13                                                                 
T  27    L    14                                                                 
I  28    E    15                                                                 
V  29    L    16                                                                 
S  30    L    17                                                                 
I  31    N    18                                                                 
L  32    E    19                                                                 
T  33    T    20                                                                 
A  34    G    21                                                                 
V  35    I    22                                                                 
G  36    D    23                                                                 
S  37    G    24                                                                 
G  38    L    25                                                                 
G  39    T    26                                                                 
L  40    T    27                                                                 
S  41    R    28                                                                 
L  42    K    29                                                                 
L  43    L    30                                                                 
A  44    A    31                                                                 
A  45    Q    32                                                                 
A  46    K    33                                                                 
G  47    L    34                                                                 
R  48    G    35                                                                 
E  49    I    36                                                                 
S  50    E    37                                                                 
K  52    Q    38                                                                 
A  53    P    39                                                                 
Y  54    T    40                                                                 
L  55    L    41                                                                 
K  56    Y    42                                                                 
K  57    W    43                                                                 
E  58    H    44                                                                 
I  59    V    45                                                                 
K  62    K    46                                                                 
G  63    N    47                                                                 
K  64    K    48                                                                 
R  65    R    49                                                                 
A  66    A    50                                                                 
V  67    L    51                                                                 
I  68    L    52                                                                 
A  69    D    53                                                                 
W  70    A    54                                                                 
M   1    L    55                                                                 
A   2    A    56                                                                 
K   3    V    57                                                                 
E   4    E    58                                                                 
TER                                                                              
END                                                                              



