
PFRMAT AL                                                                        
TARGET T0096                                                                     
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  1                                                                         
PARENT 1QGP_A                                                                    
M   1    L   126                                                                 
V   2    S   127                                                                 
I   3    S   128                                                                 
K   4    H   129                                                                 
A   5    F   130                                                                 
Q   6    Q   131                                                                 
S   7    E   132                                                                 
P   8    L   133                                                                 
A   9    S   134                                                                 
G  10    I   135                                                                 
F  11    Y   136                                                                 
A  12    Q   137                                                                 
E  13    D   138                                                                 
E  14    Q   139                                                                 
Y  15    Q   141                                                                 
I  16    R   142                                                                 
I  17    I   143                                                                 
E  18    L   144                                                                 
S  19    K   145                                                                 
I  20    F   146                                                                 
W  21    L   147                                                                 
N  23    E   148                                                                 
R  24    E   149                                                                 
F  25    L   150                                                                 
P  26    G   151                                                                 
P  27    E   152                                                                 
G  28    G   153                                                                 
T  29    K   154                                                                 
I  30    A   155                                                                 
L  31    T   156                                                                 
P  32    T   157                                                                 
A  33    A   158                                                                 
R  35    H   159                                                                 
E  36    D   160                                                                 
L  37    L   161                                                                 
S  38    S   162                                                                 
E  39    G   163                                                                 
L  40    K   164                                                                 
I  41    L   165                                                                 
G  42    G   166                                                                 
V  43    T   167                                                                 
T  44    P   168                                                                 
R  45    K   169                                                                 
T  46    K   170                                                                 
T  47    E   171                                                                 
L  48    I   172                                                                 
R  49    N   173                                                                 
E  50    R   174                                                                 
V  51    V   175                                                                 
L  52    L   176                                                                 
Q  53    Y   177                                                                 
R  54    S   178                                                                 
L  55    L   179                                                                 
A  56    A   180                                                                 
R  57    K   181                                                                 
D  58    K   182                                                                 
G  59    G   183                                                                 
W  60    K   184                                                                 
L  61    L   185                                                                 
T  62    Q   186                                                                 
I  63    K   187                                                                 
Q  64    E   188                                                                 
H  65    A   189                                                                 
G  66    G   190                                                                 
K  67    T   191                                                                 
N  72    P   192                                                                 
N  73    P   193                                                                 
F  74    L   194                                                                 
W  75    W   195                                                                 
E  76    K   196                                                                 
T  77    I   197                                                                 
S  78    A   198                                                                 
G  79    V   199                                                                 
L  80    S   200                                                                 
N  81    D   201                                                                 
TER                                                                              
END                                                                              


                          Ralf Zimmer
  LLL    LL   LL  LLLL    German Nat.Res.Center for Information Technology
 L       L L L L  L   L   Schloss Birlinghoven, D-53754 Sankt Augustin
L  LLL   L  L  L  L    L  Tel: +49-2241-14-2818, Fax: +49-2241-14-2656
 L   L   L     L  L   L   Email: Ralf.Zimmer@gmd.de
  LLL    L     L  LLLL    WWW: http://www.gmd.de/SCAI/people/zimmer.html




