
PFRMAT AL                                                                        
TARGET T0109                                                                     
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 1VSM_A                                                                    
D   4    G    56                                                                 
K   5    P    57                                                                 
Q   6    L    58                                                                 
N   7    Q    59                                                                 
L   8    I    60                                                                 
I   9    W    61                                                                 
W  10    Q    62                                                                 
I  11    T    63                                                                 
D  12    D    64                                                                 
L  13    F    65                                                                 
E  14    T    66                                                                 
M  15    L    67                                                                 
T  16    E    68                                                                 
L  18    M    71                                                                 
D  19    A    72                                                                 
I  25    W    76                                                                 
I  26    L    77                                                                 
E  27    A    78                                                                 
I  28    V    79                                                                 
A  29    T    80                                                                 
T  30    V    81                                                                 
I  31    D    82                                                                 
V  32    T    83                                                                 
T  33    A    84                                                                 
D  34    S    85                                                                 
K  35    S    86                                                                 
N  36    A    87                                                                 
L  37    I    88                                                                 
N  38    V    89                                                                 
I  39    V    90                                                                 
L  40    T    91                                                                 
A  41    Q    92                                                                 
E  42    H    93                                                                 
G  43    G    94                                                                 
P  44    R    95                                                                 
V  45    V    96                                                                 
L  46    T    97                                                                 
A  85    A   100                                                                 
E  86    A   101                                                                 
L  87    Q   102                                                                 
Q  88    H   103                                                                 
T  89    H   104                                                                 
L  90    W   105                                                                 
D  91    A   106                                                                 
F  92    T   107                                                                 
L  93    A   108                                                                 
K  94    I   109                                                                 
K  95    A   110                                                                 
W  96    V   111                                                                 
V  97    L   112                                                                 
P  98    G   113                                                                 
K  99    R   114                                                                 
G 100    P   115                                                                 
A 101    K   116                                                                 
S 102    A   117                                                                 
P 103    I   118                                                                 
I 104    K   119                                                                 
C 105    T   120                                                                 
G 106    D   121                                                                 
N 107    N   122                                                                 
S 108    G   123                                                                 
I 109    S   124                                                                 
A 110    C   125                                                                 
Q 111    F   126                                                                 
D 112    T   127                                                                 
K 113    S   128                                                                 
R 114    K   129                                                                 
F 115    S   130                                                                 
L 116    T   131                                                                 
V 117    R   132                                                                 
K 118    E   133                                                                 
Y 119    W   134                                                                 
M 120    L   135                                                                 
P 121    A   136                                                                 
D 122    R   137                                                                 
L 123    W   138                                                                 
A 124    G   139                                                                 
D 125    I   140                                                                 
Y 126    A   141                                                                 
F 127    H   142                                                                 
H 128    T   143                                                                 
Y 129    T   144                                                                 
R 130    G   145                                                                 
H 131    I   146                                                                 
L 132    P   147                                                                 
D 133    G   148                                                                 
V 134    N   149                                                                 
S 135    S   150                                                                 
T 136    Q   151                                                                 
L 137    G   152                                                                 
K 138    Q   153                                                                 
E 139    A   154                                                                 
L 140    M   155                                                                 
A 141    V   156                                                                 
A 142    E   157                                                                 
R 143    R   158                                                                 
W 144    A   159                                                                 
K 145    N   160                                                                 
P 146    R   161                                                                 
E 147    L   162                                                                 
I 148    L   163                                                                 
L 149    K   164                                                                 
E 150    D   165                                                                 
G 151    K   166                                                                 
F 152    I   167                                                                 
K 153    R   168                                                                 
N 156    M   177                                                                 
T 157    K   178                                                                 
H 158    R   179                                                                 
L 159    I   180                                                                 
A 160    P   181                                                                 
L 161    T   182                                                                 
D 162    S   183                                                                 
D 163    K   184                                                                 
I 164    Q   185                                                                 
R 165    G   186                                                                 
E 166    E   187                                                                 
S 167    L   188                                                                 
I 168    L   189                                                                 
K 169    A   190                                                                 
E 170    K   191                                                                 
L 171    A   192                                                                 
A 172    M   193                                                                 
Y 173    Y   194                                                                 
Y 174    A   195                                                                 
R 175    L   196                                                                 
E 176    N   197                                                                 
H 177    H   198                                                                 
F 178    F   199                                                                 
TER                                                                              
END                                                                              



