
PFRMAT AL                                                                        
TARGET T0101                                                                     
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  3                                                                         
PARENT 1PKL_D                                                                    
G  81    E    88                                                                 
T  82    I    89                                                                 
Y  83    R    90                                                                 
T  84    T    91                                                                 
I  85    G    92                                                                 
P  86    Q    93                                                                 
Y  87    F    94                                                                 
T  88    V    95                                                                 
Q  89    G    96                                                                 
G  90    G    97                                                                 
T  94    D    98                                                                 
I  95    A    99                                                                 
T  96    V   100                                                                 
F  97    M   101                                                                 
N  98    E   102                                                                 
K  99    R   103                                                                 
S 100    G   104                                                                 
A 105    A   105                                                                 
P 106    T   106                                                                 
I 107    C   107                                                                 
Y 108    Y   108                                                                 
V 109    V   109                                                                 
A 110    T   110                                                                 
A 111    T   111                                                                 
A 112    D   112                                                                 
N 113    K   118                                                                 
C 114    G   119                                                                 
G 115    T   120                                                                 
R 116    K   121                                                                 
A 117    D   122                                                                 
V 118    K   123                                                                 
F 119    F   124                                                                 
D 120    Y   125                                                                 
F 121    I   126                                                                 
S 122    D   127                                                                 
F 123    Y   128                                                                 
P 124    Q   129                                                                 
D 125    N   130                                                                 
S 126    L   131                                                                 
Q 127    K   133                                                                 
W 128    V   134                                                                 
V 129    V   135                                                                 
Q 130    R   136                                                                 
A 131    P   137                                                                 
S 132    G   138                                                                 
Y 133    N   139                                                                 
G 134    Y   140                                                                 
F 135    I   141                                                                 
Y 136    Y   142                                                                 
V 137    I   143                                                                 
T 138    D   144                                                                 
G 139    D   145                                                                 
D 140    G   146                                                                 
Y 141    I   147                                                                 
W 142    L   148                                                                 
Y 143    I   149                                                                 
F 144    L   150                                                                 
G 146    Q   151                                                                 
V 147    V   152                                                                 
E 148    Q   153                                                                 
V 149    S   154                                                                 
T 150    H   155                                                                 
R 151    E   156                                                                 
A 152    D   157                                                                 
G 153    E   158                                                                 
Y 154    Q   159                                                                 
Q 155    T   160                                                                 
G 156    L   161                                                                 
A 157    E   162                                                                 
Y 158    C   163                                                                 
V 159    T   164                                                                 
I 160    V   165                                                                 
G 161    T   166                                                                 
S 162    N   167                                                                 
H 163    S   168                                                                 
N 164    H   169                                                                 
T 165    T   170                                                                 
F 166    I   171                                                                 
E 167    S   172                                                                 
N 168    D   173                                                                 
T 169    R   174                                                                 
A 170    R   175                                                                 
F 171    G   176                                                                 
H 172    V   177                                                                 
H 173    N   178                                                                 
N 174    L   179                                                                 
R 175    P   180                                                                 
N 176    G   181                                                                 
T 177    C   182                                                                 
G 178    D   183                                                                 
L 179    V   184                                                                 
E 180    D   185                                                                 
I 181    L   186                                                                 
TER                                                                              
END                                                                              



