
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  1                                                                         
PARENT 1CR5_A                                                                    
M   1    H    28                                                                 
I   2    L    29                                                                 
N   3    K    30                                                                 
R   4    V    31                                                                 
T   5    S    32                                                                 
D   6    N    33                                                                 
C   7    C    34                                                                 
N   8    P    35                                                                 
E   9    N    36                                                                 
N  10    N    37                                                                 
S  11    S    38                                                                 
Y  12    Y    39                                                                 
L  13    A    40                                                                 
E  14    L    41                                                                 
D  22    A    42                                                                 
T  23    N    43                                                                 
L  24    V    44                                                                 
C  25    A    45                                                                 
F  26    A    46                                                                 
A  27    V    47                                                                 
N  28    S    48                                                                 
A  29    P    49                                                                 
G  30    N    50                                                                 
T  31    D    51                                                                 
M  32    F    52                                                                 
P  33    P    53                                                                 
V  34    N    54                                                                 
A  35    N    55                                                                 
I  36    I    56                                                                 
Y  37    Y    57                                                                 
G  38    I    58                                                                 
V  39    I    59                                                                 
N  40    I    60                                                                 
S  44    D    61                                                                 
G  45    N    62                                                                 
N  46    L    63                                                                 
N  47    F    64                                                                 
V  48    V    65                                                                 
V  49    F    66                                                                 
T  50    T    67                                                                 
L  51    T    68                                                                 
Q  52    R    69                                                                 
F  53    H    70                                                                 
Q  54    S    71                                                                 
R  55    N    72                                                                 
N  56    D    73                                                                 
L  57    I    74                                                                 
S  58    P    75                                                                 
D  59    P    76                                                                 
P  60    G    77                                                                 
R  61    T    78                                                                 
L  62    I    79                                                                 
E  63    G    80                                                                 
T  64    F    81                                                                 
I  65    N    82                                                                 
T  66    G    83                                                                 
L  67    Q    85                                                                 
Q  68    R    86                                                                 
K  69    T    87                                                                 
W  70    W    88                                                                 
G  71    G    89                                                                 
S  72    G    90                                                                 
W  73    W    91                                                                 
N  74    S    92                                                                 
P  75    L    93                                                                 
G  76    N    94                                                                 
H  77    Q    95                                                                 
I  78    D    96                                                                 
H  79    V    97                                                                 
E  80    Q    98                                                                 
I  81    A    99                                                                 
L  82    K   100                                                                 
S  83    A   101                                                                 
I  84    F   102                                                                 
R  85    D   103                                                                 
I  86    L   104                                                                 
Y  87    Y   107                                                                 
TER                                                                              
END                                                                              



