
PFRMAT AL                                                                        
TARGET T0097                                                                     
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  4                                                                         
PARENT 1A0B                                                                      
G 123    K   658                                                                 
C 124    S   659                                                                 
L 125    E   660                                                                 
P 126    A   661                                                                 
A 127    L   662                                                                 
Y 128    L   663                                                                 
D 129    D   664                                                                 
A 130    I   665                                                                 
L 131    M   667                                                                 
A 132    L   668                                                                 
G 133    E   669                                                                 
Q 134    Q   670                                                                 
F 135    Y   671                                                                 
I 136    L   672                                                                 
E 137    E   673                                                                 
A 138    L   674                                                                 
S 139    V   675                                                                 
S 140    G   676                                                                 
R 141    P   677                                                                 
E 142    K   678                                                                 
A 143    L   679                                                                 
R 144    I   680                                                                 
Q 145    T   681                                                                 
A 146    D   682                                                                 
I 147    G   683                                                                 
L 148    L   684                                                                 
K 149    A   685                                                                 
Q 150    V   686                                                                 
G 151    F   687                                                                 
Q 152    E   688                                                                 
D 153    K   689                                                                 
G 154    M   690                                                                 
L 155    M   691                                                                 
S 156    P   692                                                                 
G 157    G   693                                                                 
V 158    Y   694                                                                 
K 159    T   703                                                                 
E 160    A   704                                                                 
T 161    Q   705                                                                 
D 162    D   706                                                                 
K 163    K   707                                                                 
K 164    K   708                                                                 
W 165    G   709                                                                 
A 166    I   710                                                                 
S 167    V   711                                                                 
Q 168    E   712                                                                 
Y 169    E   713                                                                 
M 173    G   714                                                                 
G 174    H   715                                                                 
K 175    K   716                                                                 
I 176    I   717                                                                 
L 177    K   718                                                                 
D 178    G   719                                                                 
Q 179    A   720                                                                 
G 180    A   721                                                                 
E 181    G   722                                                                 
D 182    S   723                                                                 
F 183    V   724                                                                 
P 184    G   725                                                                 
A 185    L   726                                                                 
S 186    R   727                                                                 
E 187    H   728                                                                 
L 188    L   729                                                                 
A 189    Q   730                                                                 
R 190    Q   731                                                                 
I 191    L   732                                                                 
S 192    G   733                                                                 
K 193    Q   734                                                                 
L 194    Q   735                                                                 
I 195    I   736                                                                 
E 196    Q   737                                                                 
N 197    S   738                                                                 
K 198    P   739                                                                 
M 199    D   740                                                                 
S 200    L   741                                                                 
E 201    P   742                                                                 
G 202    A   743                                                                 
K 203    W   744                                                                 
K 204    E   745                                                                 
E 205    D   746                                                                 
E 206    N   747                                                                 
L 207    V   748                                                                 
Q 208    G   749                                                                 
R 209    E   750                                                                 
S 210    W   751                                                                 
L 211    I   752                                                                 
N 212    E   753                                                                 
I 213    E   754                                                                 
L 214    M   755                                                                 
T 215    K   756                                                                 
A 216    E   757                                                                 
F 217    E   758                                                                 
R 218    W   759                                                                 
K 219    R   760                                                                 
K 220    H   761                                                                 
G 221    D   762                                                                 
A 222    V   763                                                                 
E 223    E   764                                                                 
K 224    V   765                                                                 
E 225    K   767                                                                 
E 226    A   768                                                                 
L 227    W   769                                                                 
TER                                                                              
END                                                                              



