
PFRMAT AL                                                                        
TARGET T0123                                                                     
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 3BLG                                                                      
V   1    L     1                                                                 
E   2    I     2                                                                 
V   3    V     3                                                                 
T   4    T     4                                                                 
P   5    Q     5                                                                 
I   6    T     6                                                                 
M   7    M     7                                                                 
T   8    K     8                                                                 
E   9    G     9                                                                 
L  10    L    10                                                                 
D  11    D    11                                                                 
T  12    I    12                                                                 
Q  13    Q    13                                                                 
K  14    K    14                                                                 
V  15    V    15                                                                 
A  16    A    16                                                                 
G  17    G    17                                                                 
T  18    T    18                                                                 
W  19    W    19                                                                 
H  20    Y    20                                                                 
T  21    S    21                                                                 
V  22    L    22                                                                 
A  23    A    23                                                                 
M  24    M    24                                                                 
A  25    A    25                                                                 
V  26    A    26                                                                 
S  27    S    27                                                                 
D  28    D    28                                                                 
V  29    I    29                                                                 
S  30    S    30                                                                 
L  31    L    31                                                                 
L  32    L    32                                                                 
D  33    D    33                                                                 
A  34    A    34                                                                 
K  35    Q    35                                                                 
S  36    S    36                                                                 
S  37    A    37                                                                 
P  38    P    38                                                                 
L  39    L    39                                                                 
K  40    R    40                                                                 
A  41    V    41                                                                 
Y  42    Y    42                                                                 
V  43    V    43                                                                 
E  44    E    44                                                                 
G  45    E    45                                                                 
L  46    L    46                                                                 
K  47    K    47                                                                 
P  48    P    48                                                                 
T  49    T    49                                                                 
P  50    P    50                                                                 
E  51    E    51                                                                 
G  52    G    52                                                                 
D  53    D    53                                                                 
L  54    L    54                                                                 
E  55    E    55                                                                 
I  56    I    56                                                                 
L  57    L    57                                                                 
L  58    L    58                                                                 
Q  59    Q    59                                                                 
K  60    K    60                                                                 
R  61    W    61                                                                 
E  62    E    62                                                                 
N  63    N    63                                                                 
D  64    D    64                                                                 
K  65    E    65                                                                 
C  66    C    66                                                                 
A  67    A    67                                                                 
Q  68    Q    68                                                                 
E  69    K    69                                                                 
V  70    K    70                                                                 
L  71    I    71                                                                 
L  72    I    72                                                                 
A  73    A    73                                                                 
K  74    E    74                                                                 
K  75    K    75                                                                 
T  76    T    76                                                                 
D  77    K    77                                                                 
I  78    I    78                                                                 
P  79    P    79                                                                 
A  80    A    80                                                                 
V  81    V    81                                                                 
F  82    F    82                                                                 
K  83    K    83                                                                 
I  84    I    84                                                                 
N  85    D    85                                                                 
A  86    A    86                                                                 
L  87    L    87                                                                 
D  88    N    88                                                                 
E  89    E    89                                                                 
N  90    N    90                                                                 
Q  91    K    91                                                                 
L  92    V    92                                                                 
F  93    L    93                                                                 
L  94    V    94                                                                 
L  95    L    95                                                                 
D  96    D    96                                                                 
T  97    T    97                                                                 
D  98    D    98                                                                 
Y  99    Y    99                                                                 
D 100    K   100                                                                 
S 101    K   101                                                                 
H 102    Y   102                                                                 
L 103    L   103                                                                 
L 104    L   104                                                                 
L 105    F   105                                                                 
C 106    C   106                                                                 
M 107    M   107                                                                 
E 108    E   108                                                                 
N 109    N   109                                                                 
S 110    S   110                                                                 
A 111    A   111                                                                 
S 112    E   112                                                                 
P 113    P   113                                                                 
E 114    E   114                                                                 
H 115    Q   115                                                                 
S 116    S   116                                                                 
L 117    L   117                                                                 
V 118    V   118                                                                 
C 119    C   119                                                                 
Q 120    Q   120                                                                 
S 121    C   121                                                                 
L 122    L   122                                                                 
A 123    V   123                                                                 
R 124    R   124                                                                 
T 125    T   125                                                                 
L 126    P   126                                                                 
E 127    E   127                                                                 
V 128    V   128                                                                 
D 129    D   129                                                                 
D 130    D   130                                                                 
Q 131    E   131                                                                 
I 132    A   132                                                                 
R 133    L   133                                                                 
E 134    E   134                                                                 
K 135    K   135                                                                 
F 136    F   136                                                                 
E 137    D   137                                                                 
D 138    K   138                                                                 
A 139    A   139                                                                 
L 140    L   140                                                                 
K 141    K   141                                                                 
T 142    A   142                                                                 
L 143    L   143                                                                 
S 144    P   144                                                                 
V 145    M   145                                                                 
P 146    H   146                                                                 
M 147    I   147                                                                 
R 148    S   150                                                                 
I 149    F   151                                                                 
L 150    N   152                                                                 
P 151    P   153                                                                 
A 152    T   154                                                                 
Q 153    Q   155                                                                 
L 154    L   156                                                                 
E 155    E   157                                                                 
E 156    E   158                                                                 
Q 157    Q   159                                                                 
C 158    C   160                                                                 
R 159    H   161                                                                 
V 160    I   162                                                                 
TER                                                                              
END                                                                              



