
PFRMAT AL                                                                        
TARGET T0104                                                                     
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  2                                                                         
PARENT 1CTQ_A                                                                    
T  30    T     2                                                                 
E  31    E     3                                                                 
K  32    Y     4                                                                 
A  33    K     5                                                                 
I  34    L     6                                                                 
M  35    V     7                                                                 
V  36    V     8                                                                 
Y  37    V     9                                                                 
L  38    G    10                                                                 
N  39    A    11                                                                 
G  40    G    12                                                                 
D  41    G    13                                                                 
L  42    V    14                                                                 
G  43    G    15                                                                 
A  44    K    16                                                                 
T  47    S    17                                                                 
T  48    A    18                                                                 
L  49    L    19                                                                 
T  50    T    20                                                                 
R  51    I    21                                                                 
G  52    Q    22                                                                 
M  53    L    23                                                                 
L  54    I    24                                                                 
Q  55    Q    25                                                                 
G  56    N    26                                                                 
I  57    H    27                                                                 
G  58    F    28                                                                 
H  59    V    29                                                                 
Q  60    D    30                                                                 
G  61    E    31                                                                 
N  62    Y    32                                                                 
V  63    D    33                                                                 
K  64    P    34                                                                 
S  65    T    35                                                                 
P  66    I    36                                                                 
T  67    E    37                                                                 
Y  68    D    38                                                                 
T  69    S    39                                                                 
L  70    Y    40                                                                 
V  71    R    41                                                                 
E  72    K    42                                                                 
E  73    Q    43                                                                 
Y  74    V    44                                                                 
N  75    V    45                                                                 
I  76    I    46                                                                 
A  77    D    47                                                                 
G  78    G    48                                                                 
K  79    E    49                                                                 
M  80    T    50                                                                 
I  81    C    51                                                                 
Y  82    L    52                                                                 
L  86    L    53                                                                 
Y  87    D    54                                                                 
R  88    I    55                                                                 
L  89    L    56                                                                 
A  90    D    57                                                                 
D  91    T    58                                                                 
P  92    A    59                                                                 
E  93    G    60                                                                 
E  94    Q    61                                                                 
L  95    E    62                                                                 
E  96    E    63                                                                 
F  97    Y    64                                                                 
M  98    S    65                                                                 
G  99    A    66                                                                 
I 100    M    67                                                                 
R 101    R    68                                                                 
D 102    D    69                                                                 
Y 103    Q    70                                                                 
F 104    Y    71                                                                 
N 105    M    72                                                                 
T 106    R    73                                                                 
D 107    G    77                                                                 
S 108    F    78                                                                 
I 109    L    79                                                                 
C 110    C    80                                                                 
L 111    V    81                                                                 
I 112    F    82                                                                 
E 113    A    83                                                                 
L 122    I    84                                                                 
P 123    N    85                                                                 
E 124    N    86                                                                 
A 125    T    87                                                                 
D 126    K    88                                                                 
I 127    S    89                                                                 
L 128    F    90                                                                 
V 129    E    91                                                                 
N 130    D    92                                                                 
I 131    I    93                                                                 
D 132    H    94                                                                 
Y 133    Q    95                                                                 
Y 134    Y    96                                                                 
D 135    E    98                                                                 
D 136    Q    99                                                                 
A 137    I   100                                                                 
R 138    K   101                                                                 
N 139    R   102                                                                 
I 140    V   103                                                                 
E 141    L   113                                                                 
L 142    V   114                                                                 
I 143    G   115                                                                 
A 144    N   116                                                                 
Q 145    K   117                                                                 
T 146    C   118                                                                 
N 147    D   119                                                                 
L 148    L   120                                                                 
G 149    A   121                                                                 
K 150    A   122                                                                 
N 151    R   123                                                                 
I 152    T   124                                                                 
I 153    V   125                                                                 
S 154    E   126                                                                 
TER                                                                              
END                                                                              



