
PFRMAT AL                                                                        
TARGET T0125                                                                     
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 1EBD_A                                                                    
F   1    F   159                                                                 
D   2    S   160                                                                 
D   3    N   161                                                                 
V   4    R   162                                                                 
V   5    I   163                                                                 
V   6    L   164                                                                 
S   7    D   165                                                                 
R   8    S   166                                                                 
Q   9    T   167                                                                 
E  10    G   168                                                                 
Q  11    A   169                                                                 
S  12    G   173                                                                 
Y  13    E   174                                                                 
V  14    V   175                                                                 
Q  15    P   176                                                                 
R  16    K   177                                                                 
G  17    S   178                                                                 
M  18    L   179                                                                 
V  19    V   180                                                                 
N  20    V   181                                                                 
F  21    I   182                                                                 
L  22    G   183                                                                 
D  23    G   184                                                                 
E  24    G   185                                                                 
E  25    Y   186                                                                 
M  26    G   188                                                                 
H  27    I   189                                                                 
K  28    E   190                                                                 
L  29    L   191                                                                 
V  30    G   192                                                                 
K  31    T   193                                                                 
R  32    A   194                                                                 
F  33    Y   195                                                                 
R  34    A   196                                                                 
D  35    N   197                                                                 
G  41    F   198                                                                 
P  42    G   199                                                                 
G  43    T   200                                                                 
F  44    K   201                                                                 
V  45    V   202                                                                 
F  46    T   203                                                                 
L  47    I   204                                                                 
L  48    L   205                                                                 
K  49    E   206                                                                 
K  50    G   207                                                                 
V  51    A   208                                                                 
R  53    G   209                                                                 
E  54    E   210                                                                 
R  55    I   211                                                                 
M  56    L   212                                                                 
M  57    S   213                                                                 
R  58    G   214                                                                 
Y  59    F   215                                                                 
C  60    E   216                                                                 
M  61    K   217                                                                 
D  62    Q   218                                                                 
Y  63    M   219                                                                 
A  64    A   220                                                                 
R  65    A   221                                                                 
Y  66    I   222                                                                 
S  67    I   223                                                                 
K  68    K   224                                                                 
K  69    K   225                                                                 
I  70    R   226                                                                 
L  71    L   227                                                                 
Q  72    K   228                                                                 
L  73    K   229                                                                 
K  74    K   230                                                                 
H  75    G   231                                                                 
L  76    V   232                                                                 
P  77    E   233                                                                 
V  78    V   234                                                                 
N  79    V   235                                                                 
K  80    T   236                                                                 
K  81    N   237                                                                 
T  82    A   238                                                                 
L  83    L   239                                                                 
T  84    A   240                                                                 
K  85    K   241                                                                 
M  86    G   242                                                                 
G  87    A   243                                                                 
R  88    E   244                                                                 
F  89    T   251                                                                 
V  90    V   252                                                                 
G  91    T   253                                                                 
Y  92    Y   254                                                                 
R  93    E   255                                                                 
N  94    A   256                                                                 
Y  95    N   257                                                                 
G  96    G   258                                                                 
V  97    E   259                                                                 
I  98    T   260                                                                 
R  99    K   261                                                                 
E 100    T   262                                                                 
L 101    I   263                                                                 
Y 102    D   264                                                                 
A 103    A   265                                                                 
D 104    D   266                                                                 
V 105    Y   267                                                                 
F 106    V   268                                                                 
R 107    L   269                                                                 
R 140    V   270                                                                 
G 141    T   271                                                                 
TER                                                                              
END                                                                              



