
PFRMAT AL                                                                        
TARGET T0088                                                                     
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 1AVA_D                                                                    
A   1    A     1                                                                 
V   2    P     3                                                                 
S   3    P     4                                                                 
F   4    P     5                                                                 
I   5    V     6                                                                 
G   6    H     7                                                                 
S   7    D     8                                                                 
T   8    T     9                                                                 
E   9    D    10                                                                 
N  10    G    11                                                                 
D  11    H    12                                                                 
V  12    E    13                                                                 
G  13    L    14                                                                 
P  14    R    15                                                                 
S  15    A    16                                                                 
Q  16    D    17                                                                 
G  17    A    18                                                                 
S  18    N    19                                                                 
Y  19    Y    20                                                                 
S  20    Y    21                                                                 
S  21    V    22                                                                 
T  22    L    23                                                                 
H  23    S    24                                                                 
A  24    A    25                                                                 
M  25    N    26                                                                 
D  26    H    29                                                                 
N  27    G    30                                                                 
L  28    G    31                                                                 
P  29    G    32                                                                 
F  30    L    33                                                                 
V  31    T    34                                                                 
Y  32    M    35                                                                 
N  33    A    36                                                                 
T  34    P    37                                                                 
G  35    G    38                                                                 
Y  36    H    39                                                                 
N  37    G    40                                                                 
I  38    R    41                                                                 
S  49    H    42                                                                 
G  50    C    43                                                                 
G  51    P    44                                                                 
F  52    L    45                                                                 
C  53    F    46                                                                 
V  54    V    47                                                                 
G  55    S    48                                                                 
L  56    Q    49                                                                 
D  57    D    50                                                                 
G  58    P    51                                                                 
K  59    N    52                                                                 
V  60    G    53                                                                 
D  61    Q    54                                                                 
L  62    I    62                                                                 
P  63    T    63                                                                 
V  64    P    64                                                                 
V  65    Y    65                                                                 
G  66    G    66                                                                 
S  67    V    67                                                                 
L  68    A    68                                                                 
D  69    P    69                                                                 
G  70    S    70                                                                 
Q  71    D    71                                                                 
S  72    K    72                                                                 
I  73    I    73                                                                 
Y  74    I    74                                                                 
G  75    R    75                                                                 
L  76    L    76                                                                 
T  77    S    77                                                                 
E  78    T    78                                                                 
E  79    D    79                                                                 
V  80    V    80                                                                 
G  81    R    81                                                                 
L  82    I    82                                                                 
L  83    T    94                                                                 
I  84    E    95                                                                 
W  85    W    96                                                                 
M  86    H    97                                                                 
G  87    I    98                                                                 
D  88    D    99                                                                 
T  89    S   100                                                                 
N  90    E   101                                                                 
Y  91    L   102                                                                 
S  92    A   103                                                                 
R  93    A   104                                                                 
G  94    G   105                                                                 
T  95    R   106                                                                 
A  96    D   116                                                                 
M  97    P   117                                                                 
S  98    S   118                                                                 
G  99    P   119                                                                 
N 100    S   120                                                                 
S 101    G   121                                                                 
W 102    R   122                                                                 
E 103    E   123                                                                 
N 104    N   124                                                                 
V 105    A   125                                                                 
W 109    F   126                                                                 
C 110    R   127                                                                 
V 111    I   128                                                                 
G 112    E   129                                                                 
N 113    K   130                                                                 
Y 114    Y   131                                                                 
V 115    S   132                                                                 
S 116    G   133                                                                 
T 117    A   134                                                                 
Q 118    E   135                                                                 
G 119    V   136                                                                 
L 120    H   137                                                                 
S 121    E   138                                                                 
V 122    Y   139                                                                 
H 123    K   140                                                                 
V 124    L   141                                                                 
R 125    D   150                                                                 
P 126    L   151                                                                 
V 127    G   152                                                                 
I 128    V   153                                                                 
L 129    F   154                                                                 
K 130    R   155                                                                 
R 131    D   156                                                                 
N 132    L   157                                                                 
S 133    K   158                                                                 
S 134    G   160                                                                 
A 135    A   161                                                                 
Q 136    W   162                                                                 
Y 137    F   163                                                                 
S 138    L   164                                                                 
V 139    G   165                                                                 
Q 140    A   166                                                                 
K 141    T   167                                                                 
T 142    E   168                                                                 
S 143    P   169                                                                 
I 144    Y   170                                                                 
G 145    H   171                                                                 
S 146    V   172                                                                 
I 147    V   173                                                                 
R 148    V   174                                                                 
M 149    F   175                                                                 
R 150    K   176                                                                 
P 151    K   177                                                                 
Y 152    A   178                                                                 
N 153    P   179                                                                 
S 155    P   180                                                                 
S 156    A   181                                                                 
TER                                                                              
END                                                                              



