
PFRMAT AL                                                                        
TARGET T0125                                                                     
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 3LYN_A                                                                    
Q   9    I    11                                                                 
E  10    N    12                                                                 
Q  11    K    13                                                                 
S  12    A    14                                                                 
Y  13    Y    15                                                                 
V  14    E    16                                                                 
Q  15    V    17                                                                 
R  16    T    18                                                                 
G  17    M    19                                                                 
M  18    K    20                                                                 
V  19    I    21                                                                 
N  20    Q    22                                                                 
F  21    I    23                                                                 
L  22    I    24                                                                 
D  23    S    25                                                                 
E  24    G    26                                                                 
E  25    F    27                                                                 
M  26    D    28                                                                 
H  27    R    29                                                                 
K  28    Q    30                                                                 
L  29    L    31                                                                 
V  30    T    32                                                                 
K  31    A    33                                                                 
R  32    W    34                                                                 
F  33    L    35                                                                 
R  34    R    36                                                                 
D  35    V    37                                                                 
M  36    H    38                                                                 
R  37    G    39                                                                 
W  38    R    40                                                                 
N  39    R    41                                                                 
L  40    L    42                                                                 
G  41    T    43                                                                 
P  42    N    44                                                                 
G  43    N    45                                                                 
F  44    Q    46                                                                 
V  45    K    47                                                                 
F  46    K    48                                                                 
L  47    T    49                                                                 
L  48    L    50                                                                 
K  49    F    51                                                                 
K  50    F    52                                                                 
V  51    V    53                                                                 
N  52    N    54                                                                 
R  53    R    55                                                                 
E  54    R    56                                                                 
R  55    Y    57                                                                 
M  56    M    58                                                                 
M  57    Q    59                                                                 
R  58    T    60                                                                 
Y  59    H    61                                                                 
C  60    W    62                                                                 
M  61    Q    63                                                                 
D  62    N    64                                                                 
Y  63    Y    65                                                                 
A  64    M    66                                                                 
R  65    L    67                                                                 
Y  66    W    68                                                                 
S  67    V    69                                                                 
K  68    K    70                                                                 
K  69    R    71                                                                 
I  70    K    72                                                                 
L  71    I    73                                                                 
Q  72    K    74                                                                 
L  73    A    75                                                                 
K  74    L    76                                                                 
H  75    G    77                                                                 
L  76    R    78                                                                 
P  77    P    79                                                                 
V  78    A    80                                                                 
N  79    A    81                                                                 
K  80    V    82                                                                 
K  81    G    83                                                                 
T  82    D    84                                                                 
L  83    Y    85                                                                 
T  84    T    86                                                                 
K  85    R    87                                                                 
M  86    L    88                                                                 
G  87    G    89                                                                 
R  88    A    90                                                                 
F  89    E    91                                                                 
V  90    I    92                                                                 
G  91    G    93                                                                 
Y  92    R    94                                                                 
R  93    R    95                                                                 
N  94    V    96                                                                 
Y  95    D    97                                                                 
G  96    M    98                                                                 
V  97    V    99                                                                 
A 103    F   100                                                                 
D 104    F   101                                                                 
V 105    Y   102                                                                 
F 106    N   103                                                                 
R 107    F   104                                                                 
D 108    L   105                                                                 
V 109    S   106                                                                 
Q 110    G   107                                                                 
G 111    R   108                                                                 
F 112    K   109                                                                 
R 113    M   110                                                                 
G 114    I   111                                                                 
P 115    P   112                                                                 
K 116    P   113                                                                 
M 117    Y   114                                                                 
T 118    S   115                                                                 
A 119    A   116                                                                 
A 120    Y   117                                                                 
M 121    M   118                                                                 
R 122    A   119                                                                 
K 123    K   120                                                                 
Y 124    L   121                                                                 
S 125    N   122                                                                 
S 126    A   123                                                                 
K 127    L   124                                                                 
D 128    R   125                                                                 
P 129    P   126                                                                 
G 130    A   127                                                                 
T 131    D   128                                                                 
F 132    V   129                                                                 
P 133    P   130                                                                 
C 134    V   131                                                                 
K 135    K   132                                                                 
TER                                                                              
END                                                                              



