
PFRMAT AL                                                                        
TARGET T0120                                                                     
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 1CUN_A                                                                    
N 112    Q   116                                                                 
L 113    F   117                                                                 
E 114    A   119                                                                 
K 115    N   120                                                                 
V 116    V   121                                                                 
E 117    E   122                                                                 
N 118    E   123                                                                 
P 119    E   124                                                                 
A 120    E   125                                                                 
E 121    A   126                                                                 
V 122    W   127                                                                 
I 123    I   128                                                                 
R 124    N   129                                                                 
E 125    E   130                                                                 
L 126    K   131                                                                 
I 127    M   132                                                                 
C 128    T   133                                                                 
Y 129    V   135                                                                 
C 130    A   136                                                                 
L 131    S   137                                                                 
D 132    E   138                                                                 
T 133    D   139                                                                 
I 134    Y   140                                                                 
A 135    G   141                                                                 
E 136    D   142                                                                 
N 137    T   143                                                                 
Q 138    L   144                                                                 
A 139    A   145                                                                 
K 140    A   146                                                                 
N 141    I   147                                                                 
E 142    Q   148                                                                 
H 143    G   149                                                                 
L 144    L   150                                                                 
Q 145    L   151                                                                 
K 146    K   152                                                                 
E 147    K   153                                                                 
N 148    H   154                                                                 
E 149    E   155                                                                 
R 150    A   156                                                                 
L 151    F   157                                                                 
L 152    E   158                                                                 
R 153    T   159                                                                 
D 154    D   160                                                                 
W 155    F   161                                                                 
N 156    T   162                                                                 
D 157    V   163                                                                 
V 158    H   164                                                                 
Q 159    K   165                                                                 
G 160    D   166                                                                 
R 161    R   167                                                                 
F 162    V   168                                                                 
E 163    N   169                                                                 
K 164    D   170                                                                 
C 165    C   172                                                                 
V 166    A   173                                                                 
S 167    N   174                                                                 
A 168    G   175                                                                 
K 169    E   176                                                                 
E 170    D   177                                                                 
A 171    L   178                                                                 
L 172    I   179                                                                 
E 173    K   180                                                                 
T 174    K   181                                                                 
Y 177    N   182                                                                 
K 178    N   183                                                                 
R 179    H   184                                                                 
F 180    H   185                                                                 
I 181    V   186                                                                 
L 182    E   187                                                                 
V 183    N   188                                                                 
L 184    I   189                                                                 
N 185    T   190                                                                 
E 186    A   191                                                                 
K 187    K   192                                                                 
K 188    M   193                                                                 
T 189    K   194                                                                 
K 190    G   195                                                                 
I 191    L   196                                                                 
R 192    K   197                                                                 
S 193    G   198                                                                 
L 194    K   199                                                                 
H 195    V   200                                                                 
N 196    S   201                                                                 
K 197    D   202                                                                 
L 198    L   203                                                                 
L 199    E   204                                                                 
N 200    K   205                                                                 
A 201    A   206                                                                 
A 202    A   207                                                                 
Q 203    A   208                                                                 
E 204    Q   209                                                                 
R 205    R   210                                                                 
E 206    K   211                                                                 
K 207    A   212                                                                 
D 208    K   213                                                                 
I 209    L   214                                                                 
K 210    D   215                                                                 
Q 211    E   216                                                                 
E 212    N   217                                                                 
G 213    S   218                                                                 
E 214    A   219                                                                 
TER                                                                              
END                                                                              



