
PFRMAT AL                                                                        
TARGET T0110                                                                     
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 1A0R_P                                                                    
M   1    M    72                                                                 
A   2    S    73                                                                 
R   3    Q    75                                                                 
E   4    E    76                                                                 
F   5    Y    77                                                                 
K   6    E    78                                                                 
R   7    L    79                                                                 
S   8    D    86                                                                 
D   9    E    87                                                                 
R  10    N    88                                                                 
V  11    C    89                                                                 
A  12    L    90                                                                 
Q  13    R    91                                                                 
E  14    K    92                                                                 
I  15    Y    93                                                                 
Q  16    R    94                                                                 
K  17    R    95                                                                 
E  18    Q    96                                                                 
I  19    C    97                                                                 
A  20    M    98                                                                 
V  21    Q    99                                                                 
I  22    D   100                                                                 
L  23    M   101                                                                 
Q  24    H   102                                                                 
R  25    Q   103                                                                 
E  26    K   104                                                                 
V  27    S   106                                                                 
K  28    F   107                                                                 
D  29    G   108                                                                 
P  30    P   109                                                                 
R  31    R   110                                                                 
I  32    Y   111                                                                 
G  33    G   112                                                                 
M  34    F   113                                                                 
V  35    V   114                                                                 
T  36    Y   115                                                                 
V  37    E   116                                                                 
S  38    L   117                                                                 
S  43    E   118                                                                 
S  44    S   119                                                                 
D  45    G   120                                                                 
L  46    E   121                                                                 
S  47    Q   122                                                                 
Y  48    F   123                                                                 
A  49    L   124                                                                 
K  50    E   125                                                                 
I  51    T   126                                                                 
F  52    I   136                                                                 
V  53    V   137                                                                 
T  54    V   138                                                                 
F  55    H   139                                                                 
L  56    I   140                                                                 
F  57    Y   141                                                                 
D  58    E   142                                                                 
H  59    D   143                                                                 
D  60    G   144                                                                 
E  61    I   145                                                                 
M  62    K   146                                                                 
A  63    G   147                                                                 
I  64    L   151                                                                 
E  65    N   152                                                                 
Q  66    S   153                                                                 
G  67    S   154                                                                 
M  68    L   155                                                                 
K  69    I   156                                                                 
G  70    C   157                                                                 
L  71    L   158                                                                 
E  72    A   159                                                                 
K  73    A   160                                                                 
A  74    E   161                                                                 
S  75    Y   162                                                                 
P  76    P   163                                                                 
Y  77    M   164                                                                 
I  78    V   165                                                                 
R  79    K   166                                                                 
S  80    F   167                                                                 
L  81    C   168                                                                 
L  82    K   169                                                                 
G  83    I   170                                                                 
K  84    K   171                                                                 
A  85    A   172                                                                 
M  86    S   173                                                                 
R  87    N   174                                                                 
L  88    S   183                                                                 
R  89    D   184                                                                 
I  90    V   185                                                                 
V  91    L   186                                                                 
P  92    P   187                                                                 
E  93    T   188                                                                 
I  94    L   189                                                                 
R  95    L   190                                                                 
F  96    V   191                                                                 
I  97    Y   192                                                                 
Y  98    K   193                                                                 
D  99    G   195                                                                 
Q 100    E   196                                                                 
S 101    L   197                                                                 
L 102    L   198                                                                 
V 103    S   199                                                                 
E 104    N   200                                                                 
G 105    F   201                                                                 
M 106    I   202                                                                 
R 107    S   203                                                                 
M 108    V   204                                                                 
S 109    T   205                                                                 
N 110    E   206                                                                 
L 111    L   208                                                                 
V 112    A   209                                                                 
T 113    E   210                                                                 
N 114    E   211                                                                 
V 115    F   212                                                                 
V 116    F   213                                                                 
R 117    T   214                                                                 
E 118    G   215                                                                 
D 119    D   216                                                                 
E 120    V   217                                                                 
K 121    E   218                                                                 
K 122    S   219                                                                 
H 123    F   220                                                                 
V 124    L   221                                                                 
E 125    N   222                                                                 
E 126    E   223                                                                 
S 127    Y   224                                                                 
N 128    G   225                                                                 
TER                                                                              
END                                                                              



