
PFRMAT AL                                                                        
TARGET T0118                                                                     
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 1CVJ_C                                                                    
F  63    L    13                                                                 
V  64    Y    14                                                                 
E  65    V    15                                                                 
K  67    G    16                                                                 
G  68    D    17                                                                 
L  69    L    18                                                                 
W  70    H    19                                                                 
E  71    P    20                                                                 
S  72    D    21                                                                 
D  73    V    22                                                                 
D  74    T    23                                                                 
R  75    E    24                                                                 
K  76    A    25                                                                 
K  77    M    26                                                                 
H  78    L    27                                                                 
L  79    Y    28                                                                 
L  80    K    30                                                                 
I  81    F    31                                                                 
R  82    S    32                                                                 
E  83    P    33                                                                 
Q  84    A    34                                                                 
H  85    G    35                                                                 
P  86    P    36                                                                 
E  87    I    37                                                                 
L  88    L    38                                                                 
D  89    S    39                                                                 
I  90    I    40                                                                 
R  91    R    41                                                                 
I  92    V    42                                                                 
V  93    C    43                                                                 
F  94    R    44                                                                 
S  95    D    45                                                                 
S  96    M    46                                                                 
S  97    I    47                                                                 
R  98    T    48                                                                 
T  99    R    49                                                                 
K 100    R    50                                                                 
P 106    S    51                                                                 
T 107    L    52                                                                 
S 108    G    53                                                                 
Y 109    Y    54                                                                 
G 110    A    55                                                                 
E 111    Y    56                                                                 
F 112    V    57                                                                 
C 113    N    58                                                                 
K 115    F    59                                                                 
H 116    Q    60                                                                 
G 117    Q    61                                                                 
I 118    P    62                                                                 
K 119    A    63                                                                 
F 120    D    64                                                                 
A 121    A    65                                                                 
D 122    E    66                                                                 
K 123    R    67                                                                 
L 124    A    68                                                                 
I 125    L    69                                                                 
I 130    D    70                                                                 
K 131    T    71                                                                 
E 132    M    72                                                                 
P 133    N    73                                                                 
K 134    F    74                                                                 
K 135    D    75                                                                 
E 136    V    76                                                                 
V 137    I    77                                                                 
P 138    K    78                                                                 
F 139    G    79                                                                 
D 140    K    80                                                                 
R 141    R    83                                                                 
L 142    I    84                                                                 
K 143    M    85                                                                 
R 144    W    86                                                                 
K 145    S    87                                                                 
G 146    Q    88                                                                 
G 147    R    89                                                                 
K 148    D    90                                                                 
TER                                                                              
END                                                                              



