
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  2                                                                         
PARENT 1DLX_A                                                                    
E  20    D    91                                                                 
D  21    E    92                                                                 
K  22    T    93                                                                 
V  23    T    94                                                                 
S  24    Y    95                                                                 
K  25    E    96                                                                 
Q  26    R    97                                                                 
L  27    L    98                                                                 
E  28    A    99                                                                 
S  29    E   100                                                                 
K  30    E   101                                                                 
G  31    T   102                                                                 
I  32    L   103                                                                 
K  33    A   107                                                                 
F  34    E   108                                                                 
E  35    F   109                                                                 
Y  36    F   110                                                                 
E  37    E   111                                                                 
E  38    D   112                                                                 
W  39    A   114                                                                 
K  40    D   115                                                                 
V  41    K   116                                                                 
P  42    P   117                                                                 
Y  43    Y   118                                                                 
V  44    T   119                                                                 
I  45    F   120                                                                 
P  46    E   121                                                                 
A  47    D   122                                                                 
S  48    Y   123                                                                 
N  49    D   124                                                                 
H  50    V   125                                                                 
T  51    S   126                                                                 
Y  52    F   127                                                                 
T  53    G   128                                                                 
P  54    S   129                                                                 
D  55    G   130                                                                 
G  61    V   131                                                                 
I  62    L   132                                                                 
F  63    T   133                                                                 
V  64    V   134                                                                 
E  65    K   135                                                                 
T  66    L   136                                                                 
K  67    G   137                                                                 
G  68    G   138                                                                 
L  69    D   139                                                                 
K  76    L   140                                                                 
K  77    G   141                                                                 
H  78    T   142                                                                 
L  79    Y   143                                                                 
L  80    V   144                                                                 
I  81    I   145                                                                 
R  82    N   146                                                                 
E  83    K   147                                                                 
Q  84    Q   148                                                                 
H  85    T   149                                                                 
P  86    P   150                                                                 
E  87    N   151                                                                 
L  88    K   152                                                                 
D  89    Q   153                                                                 
I  90    I   154                                                                 
R  91    W   155                                                                 
I  92    L   156                                                                 
V  93    S   157                                                                 
F  94    S   158                                                                 
S  95    P   159                                                                 
S  96    S   160                                                                 
S  97    S   161                                                                 
R  98    G   162                                                                 
T  99    P   163                                                                 
K 100    K   164                                                                 
L 101    R   165                                                                 
Y 102    Y   166                                                                 
K 103    D   167                                                                 
G 104    W   168                                                                 
S 105    T   169                                                                 
P 106    G   170                                                                 
T 107    K   171                                                                 
S 108    N   172                                                                 
E 111    W   173                                                                 
F 112    V   174                                                                 
C 113    Y   175                                                                 
E 114    S   176                                                                 
K 115    H   177                                                                 
H 116    D   178                                                                 
G 117    G   179                                                                 
I 118    V   180                                                                 
K 119    S   181                                                                 
F 120    L   182                                                                 
A 121    H   183                                                                 
D 122    E   184                                                                 
L 124    L   185                                                                 
I 125    L   186                                                                 
P 126    A   187                                                                 
A 127    A   188                                                                 
E 128    E   189                                                                 
W 129    L   190                                                                 
I 130    T   191                                                                 
K 131    K   192                                                                 
E 132    A   193                                                                 
P 133    L   194                                                                 
K 134    K   195                                                                 
K 135    T   196                                                                 
E 136    K   197                                                                 
V 137    L   198                                                                 
P 138    D   199                                                                 
F 139    L   200                                                                 
D 140    S   201                                                                 
R 141    S   202                                                                 
L 142    L   203                                                                 
K 143    A   204                                                                 
R 144    Y   205                                                                 
K 145    S   206                                                                 
G 146    G   207                                                                 
G 147    K   208                                                                 
K 148    D   209                                                                 
K 149    A   210                                                                 
TER                                                                              
END                                                                              



