
PFRMAT AL                                                                        
TARGET T0096                                                                     
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 1EGA_B                                                                    
E  34    D     4                                                                 
R  35    K     5                                                                 
E  36    S     6                                                                 
L  37    Y     7                                                                 
S  38    C     8                                                                 
E  39    G     9                                                                 
L  40    F    10                                                                 
I  41    I    11                                                                 
G  42    A    12                                                                 
V  43    I    13                                                                 
T  44    V    14                                                                 
R  45    N    18                                                                 
T  46    V    19                                                                 
T  47    G    20                                                                 
L  48    K    21                                                                 
R  49    S    22                                                                 
E  50    T    23                                                                 
V  51    L    24                                                                 
L  52    L    25                                                                 
Q  53    N    26                                                                 
R  54    K    27                                                                 
L  55    L    28                                                                 
A  56    L    29                                                                 
D  58    G    30                                                                 
G  59    Q    31                                                                 
W  60    K    32                                                                 
L  61    I    33                                                                 
T  62    S    34                                                                 
I  63    I    35                                                                 
Q  64    T    36                                                                 
H  65    S    37                                                                 
G  66    R    38                                                                 
K  67    K    39                                                                 
P  68    A    40                                                                 
T  69    Q    41                                                                 
K  70    T    42                                                                 
V  71    T    43                                                                 
N  72    R    44                                                                 
N  73    I    59                                                                 
F  74    Y    60                                                                 
W  75    V    61                                                                 
E  76    D    62                                                                 
T  77    T    63                                                                 
S  78    P    64                                                                 
G  79    G    65                                                                 
L  80    L    66                                                                 
N  81    H    67                                                                 
I  82    M    68                                                                 
L  83    E    69                                                                 
E  84    E    70                                                                 
T  85    A    73                                                                 
L  86    I    74                                                                 
A  87    N    75                                                                 
R  88    R    76                                                                 
L  89    L    77                                                                 
D  90    M    78                                                                 
H  91    N    79                                                                 
E  92    K    80                                                                 
S  93    A    81                                                                 
V  94    A    82                                                                 
P  95    S    83                                                                 
Q  96    S    84                                                                 
L  97    S    85                                                                 
I  98    I    86                                                                 
D  99    G    87                                                                 
N 100    D    88                                                                 
L 101    V    89                                                                 
L 102    E    90                                                                 
S 109    L    91                                                                 
T 110    V    92                                                                 
I 111    I    93                                                                 
F 112    F    94                                                                 
I 113    V    95                                                                 
R 114    V    96                                                                 
T 115    E    97                                                                 
A 116    G    98                                                                 
F 117    T    99                                                                 
R 118    R   100                                                                 
Q 119    W   101                                                                 
H 120    T   102                                                                 
P 121    P   103                                                                 
K 123    D   104                                                                 
A 124    D   105                                                                 
Q 125    E   106                                                                 
E 126    M   107                                                                 
V 127    V   108                                                                 
L 128    L   109                                                                 
A 129    N   110                                                                 
T 130    K   111                                                                 
A 131    V   126                                                                 
N 132    D   127                                                                 
E 133    N   128                                                                 
V 134    V   129                                                                 
A 135    Q   130                                                                 
D 136    E   131                                                                 
H 137    K   132                                                                 
A 138    A   133                                                                 
D 139    D   134                                                                 
A 140    L   135                                                                 
F 141    L   136                                                                 
A 142    P   137                                                                 
E 143    H   138                                                                 
L 144    L   139                                                                 
D 145    Q   140                                                                 
Y 146    F   141                                                                 
N 147    L   142                                                                 
F 149    A   143                                                                 
R 150    S   144                                                                 
G 151    Q   145                                                                 
L 152    M   146                                                                 
A 153    N   147                                                                 
F 154    F   148                                                                 
A 155    V   152                                                                 
S 156    P   153                                                                 
G 157    I   154                                                                 
N 158    S   155                                                                 
P 159    A   156                                                                 
I 160    E   157                                                                 
Y 161    T   158                                                                 
G 162    G   159                                                                 
L 163    L   160                                                                 
I 164    N   161                                                                 
L 165    V   162                                                                 
N 166    D   163                                                                 
G 167    T   164                                                                 
M 168    I   165                                                                 
K 169    A   166                                                                 
G 170    A   167                                                                 
L 171    I   168                                                                 
Y 172    V   169                                                                 
T 173    R   170                                                                 
R 174    P   174                                                                 
I 175    E   175                                                                 
G 176    A   176                                                                 
R 177    T   177                                                                 
H 178    H   178                                                                 
Y 179    H   179                                                                 
F 180    F   180                                                                 
A 181    P   181                                                                 
N 182    E   182                                                                 
TER                                                                              
END                                                                              



