
PFRMAT AL                                                                        
TARGET T0091                                                                     
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 1SES_B                                                                    
M   1    A    24                                                                 
F   2    L    25                                                                 
G   3    D    26                                                                 
K   4    L    27                                                                 
G   5    E    28                                                                 
G   6    A    29                                                                 
L   7    L    30                                                                 
G   8    L    31                                                                 
G   9    A    32                                                                 
L  10    L    33                                                                 
M  11    D    34                                                                 
K  12    R    35                                                                 
Q  13    E    36                                                                 
A  14    V    37                                                                 
Q  15    Q    38                                                                 
Q  16    E    39                                                                 
M  17    L    40                                                                 
Q  18    K    41                                                                 
E  19    K    42                                                                 
K  20    R    43                                                                 
M  21    L    44                                                                 
Q  22    Q    45                                                                 
K  23    E    46                                                                 
M  24    V    47                                                                 
Q  25    Q    48                                                                 
E  26    T    49                                                                 
E  27    E    50                                                                 
I  28    R    51                                                                 
A  29    N    52                                                                 
Q  30    Q    53                                                                 
L  31    V    54                                                                 
E  32    A    55                                                                 
R  53    K    56                                                                 
R  54    R    57                                                                 
I  55    V    58                                                                 
D  56    P    59                                                                 
I  57    K    60                                                                 
D  58    A    61                                                                 
P  59    P    62                                                                 
S  60    P    63                                                                 
D  64    E    64                                                                 
D  65    E    65                                                                 
K  66    K    66                                                                 
E  67    E    67                                                                 
M  68    A    68                                                                 
L  69    L    69                                                                 
E  70    I    70                                                                 
D  71    A    71                                                                 
I  73    R    72                                                                 
A  74    G    73                                                                 
A  75    K    74                                                                 
A  76    A    75                                                                 
F  77    L    76                                                                 
N  78    G    77                                                                 
D  79    E    78                                                                 
A  80    E    79                                                                 
V  81    A    80                                                                 
R  82    K    81                                                                 
R  83    R    82                                                                 
A  84    L    83                                                                 
E  85    E    84                                                                 
E  86    E    85                                                                 
L  87    A    86                                                                 
Q  88    L    87                                                                 
K  89    R    88                                                                 
E  90    E    89                                                                 
K  91    K    90                                                                 
M  92    E    91                                                                 
A  93    A    92                                                                 
S  94    R    93                                                                 
V  95    L    94                                                                 
T  96    E    95                                                                 
A  97    A    96                                                                 
G  98    Q   100                                                                 
M  99    V   101                                                                 
P 100    P   102                                                                 
L 101    L   103                                                                 
P 102    P   104                                                                 
P 103    P   105                                                                 
G 104    W   106                                                                 
M 105    P   107                                                                 
K 106    G   108                                                                 
F 107    A   109                                                                 
P 108    P   110                                                                 
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




