
PFRMAT AL                                                                        
TARGET T0118                                                                     
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 1TRB                                                                      
L  19    L   119                                                                 
E  20    G   120                                                                 
D  21    L   121                                                                 
K  22    P   122                                                                 
V  23    S   123                                                                 
S  24    E   124                                                                 
K  25    E   125                                                                 
Q  26    A   126                                                                 
L  27    F   127                                                                 
E  28    K   128                                                                 
S  29    G   129                                                                 
K  30    R   130                                                                 
G  31    G   131                                                                 
I  32    V   132                                                                 
K  33    S   133                                                                 
F  34    A   134                                                                 
E  35    D   139                                                                 
Y  36    G   140                                                                 
E  37    F   141                                                                 
E  38    F   142                                                                 
W  39    Y   143                                                                 
K  40    R   144                                                                 
V  41    N   145                                                                 
P  42    Q   146                                                                 
Y  43    K   147                                                                 
V  44    V   148                                                                 
I  45    A   149                                                                 
P  46    V   150                                                                 
Y  52    I   151                                                                 
T  53    G   152                                                                 
P  54    G   153                                                                 
D  55    G   154                                                                 
F  56    N   155                                                                 
L  57    T   156                                                                 
L  58    L   164                                                                 
P  59    S   165                                                                 
N  60    N   166                                                                 
G  61    I   167                                                                 
I  62    H   172                                                                 
F  63    L   173                                                                 
V  64    I   174                                                                 
E  65    H   175                                                                 
T  66    R   176                                                                 
K  67    R   177                                                                 
G  68    D   178                                                                 
L  69    G   179                                                                 
W  70    F   180                                                                 
E  71    R   181                                                                 
S  72    A   182                                                                 
D  73    E   183                                                                 
D  74    K   184                                                                 
R  75    I   185                                                                 
K  76    I   187                                                                 
K  77    K   188                                                                 
H  78    R   189                                                                 
L  79    L   190                                                                 
L  80    M   191                                                                 
I  81    D   192                                                                 
R  82    K   193                                                                 
E  83    V   194                                                                 
Q  84    E   195                                                                 
H  85    N   196                                                                 
P  86    G   197                                                                 
E  87    N   198                                                                 
I  90    I   199                                                                 
R  91    I   200                                                                 
I  92    L   201                                                                 
V  93    H   202                                                                 
F  94    T   203                                                                 
S  95    N   204                                                                 
S  96    R   205                                                                 
S  97    T   206                                                                 
R  98    L   207                                                                 
T  99    E   208                                                                 
K 100    E   209                                                                 
L 101    V   210                                                                 
Y 102    T   211                                                                 
K 103    G   212                                                                 
G 104    Q   214                                                                 
S 105    M   215                                                                 
P 106    G   216                                                                 
T 107    V   217                                                                 
S 108    T   218                                                                 
Y 109    G   219                                                                 
G 110    V   220                                                                 
E 111    R   221                                                                 
F 112    L   222                                                                 
C 113    R   223                                                                 
E 114    D   224                                                                 
K 115    T   225                                                                 
H 116    Q   226                                                                 
G 117    N   227                                                                 
I 118    S   228                                                                 
K 119    D   229                                                                 
F 120    N   230                                                                 
A 121    I   231                                                                 
D 122    E   232                                                                 
K 123    S   233                                                                 
L 124    L   234                                                                 
I 125    D   235                                                                 
P 126    V   236                                                                 
A 127    A   237                                                                 
E 128    G   238                                                                 
W 129    L   239                                                                 
I 130    F   240                                                                 
K 131    V   241                                                                 
R 144    A   242                                                                 
K 145    I   243                                                                 
G 146    G   244                                                                 
TER                                                                              
END                                                                              



