
PFRMAT AL                                                                        
TARGET T0114                                                                     
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 1QR4_A                                                                    
Y  12    G    93                                                                 
L  13    I    94                                                                 
E  14    S    95                                                                 
I  15    F    96                                                                 
H  16    S    97                                                                 
N  17    D    98                                                                 
N  18    I    99                                                                 
E  19    E   101                                                                 
G  20    N   102                                                                 
R  21    S   103                                                                 
D  22    A   104                                                                 
T  23    T   105                                                                 
L  24    V   106                                                                 
C  25    S   107                                                                 
F  26    W   108                                                                 
A  27    T   109                                                                 
N  28    P   110                                                                 
A  29    P   111                                                                 
G  30    S   113                                                                 
T  31    R   114                                                                 
M  32    V   115                                                                 
P  33    D   116                                                                 
V  34    S   117                                                                 
A  35    Y   118                                                                 
I  36    R   119                                                                 
Y  37    V   120                                                                 
G  38    S   121                                                                 
V  39    Y   122                                                                 
N  40    V   123                                                                 
W  41    P   124                                                                 
V  42    I   125                                                                 
E  43    T   126                                                                 
S  44    G   127                                                                 
G  45    T   129                                                                 
N  46    P   130                                                                 
N  47    N   131                                                                 
V  48    V   132                                                                 
V  49    V   133                                                                 
T  50    T   134                                                                 
L  51    V   135                                                                 
Q  52    D   136                                                                 
F  53    G   137                                                                 
Q  54    S   138                                                                 
L  62    K   139                                                                 
E  63    T   140                                                                 
T  64    R   141                                                                 
I  65    T   142                                                                 
T  66    K   143                                                                 
L  67    L   144                                                                 
Q  68    V   145                                                                 
K  69    K   146                                                                 
W  73    L   147                                                                 
N  74    V   148                                                                 
P  75    P   149                                                                 
G  76    G   150                                                                 
H  77    V   151                                                                 
I  78    D   152                                                                 
H  79    Y   153                                                                 
E  80    N   156                                                                 
I  81    I   157                                                                 
L  82    I   158                                                                 
S  83    S   159                                                                 
I  84    V   160                                                                 
R  85    K   161                                                                 
I  86    G   162                                                                 
Y  87    F   163                                                                 
TER                                                                              
END                                                                              



