
PFRMAT AL                                                                        
TARGET T0108                                                                     
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 1CWV_A                                                                    
V  91    L   503                                                                 
R  92    T   504                                                                 
I  93    L   505                                                                 
S  94    T   506                                                                 
A  95    A   507                                                                 
D  96    A   508                                                                 
I  97    V   509                                                                 
W  98    I   510                                                                 
G  99    G   511                                                                 
Q 100    D   512                                                                 
N 103    G   513                                                                 
I 104    A   514                                                                 
Y 105    P   515                                                                 
G 106    A   516                                                                 
D 107    N   517                                                                 
T 108    G   518                                                                 
K 109    K   519                                                                 
T 118    T   520                                                                 
P 119    A   521                                                                 
V 120    I   522                                                                 
N 121    T   523                                                                 
V 122    V   524                                                                 
S 123    E   525                                                                 
I 124    F   526                                                                 
A 125    T   527                                                                 
A 126    V   528                                                                 
I 127    A   529                                                                 
P 128    D   530                                                                 
Q 129    F   531                                                                 
S 130    E   532                                                                 
S 131    G   533                                                                 
G 134    K   534                                                                 
W 135    P   535                                                                 
G 136    L   536                                                                 
N 137    A   537                                                                 
P 138    G   538                                                                 
T 139    Q   539                                                                 
R 140    E   540                                                                 
A 141    V   541                                                                 
R 142    V   542                                                                 
I 143    I   543                                                                 
V 144    T   544                                                                 
W 145    T   545                                                                 
T 146    N   546                                                                 
N 147    N   547                                                                 
N 148    K   553                                                                 
F 149    I   554                                                                 
V 150    T   555                                                                 
A 151    E   556                                                                 
Q 152    K   557                                                                 
T 153    T   558                                                                 
D 154    D   559                                                                 
G 155    A   560                                                                 
T 156    N   561                                                                 
Y 157    G   562                                                                 
K 158    V   563                                                                 
A 159    A   564                                                                 
T 160    R   565                                                                 
L 161    I   566                                                                 
T 162    A   567                                                                 
I 163    L   568                                                                 
S 164    T   569                                                                 
T 165    N   570                                                                 
D 167    T   571                                                                 
S 168    T   572                                                                 
P 169    D   573                                                                 
N 170    G   574                                                                 
F 171    V   575                                                                 
N 172    T   576                                                                 
T 173    V   577                                                                 
I 174    V   578                                                                 
A 175    T   579                                                                 
T 176    A   580                                                                 
D 177    E   581                                                                 
A 178    V   582                                                                 
A 179    E   583                                                                 
D 180    G   584                                                                 
S 181    Q   585                                                                 
V 182    R   586                                                                 
V 183    Q   587                                                                 
T 184    S   588                                                                 
N 185    V   589                                                                 
M 186    D   590                                                                 
I 187    T   591                                                                 
L 188    H   592                                                                 
F 189    F   593                                                                 
V 190    V   594                                                                 
G 191    K   595                                                                 
S 192    G   596                                                                 
TER                                                                              
END                                                                              



