
PFRMAT AL                                                                        
TARGET T0107                                                                     
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 2SNV                                                                      
P   9    R   114                                                                 
V  10    L   115                                                                 
V  43    F   116                                                                 
R  44    D   117                                                                 
V  45    V   118                                                                 
L  46    K   119                                                                 
W  47    N   120                                                                 
D  48    E   121                                                                 
E  49    D   122                                                                 
N  50    G   123                                                                 
Y  51    D   124                                                                 
L  52    V   125                                                                 
Y  53    I   126                                                                 
V  54    G   127                                                                 
L  55    H   128                                                                 
A  56    A   129                                                                 
I  57    L   130                                                                 
V  58    A   131                                                                 
K  59    M   132                                                                 
D  60    E   133                                                                 
P  61    G   134                                                                 
V  62    K   135                                                                 
L  63    V   136                                                                 
N  64    M   137                                                                 
K  65    P   139                                                                 
D  66    L   140                                                                 
N  67    H   141                                                                 
S  68    V   142                                                                 
N  69    K   143                                                                 
P  70    G   144                                                                 
W  71    T   145                                                                 
E  72    I   146                                                                 
I  80    D   147                                                                 
D  81    H   148                                                                 
E  82    P   149                                                                 
N  83    V   150                                                                 
N  84    L   151                                                                 
H  85    S   152                                                                 
K  86    K   153                                                                 
T  87    L   154                                                                 
G  88    K   155                                                                 
Y  89    F   156                                                                 
Y  90    T   157                                                                 
E  91    K   158                                                                 
D  92    S   159                                                                 
D  93    S   160                                                                 
D  94    A   161                                                                 
A  95    Y   162                                                                 
Q  96    D   163                                                                 
F  97    M   164                                                                 
R  98    E   165                                                                 
V  99    F   166                                                                 
N 100    A   167                                                                 
Y 101    Q   168                                                                 
M 102    L   169                                                                 
N 103    R   174                                                                 
E 104    S   175                                                                 
Q 105    E   176                                                                 
T 106    A   177                                                                 
F 107    F   178                                                                 
G 108    T   179                                                                 
T 109    Y   180                                                                 
G 110    T   181                                                                 
G 111    S   182                                                                 
S 112    E   183                                                                 
P 113    E   186                                                                 
A 114    G   187                                                                 
R 115    F   188                                                                 
F 116    Y   189                                                                 
K 117    H   193                                                                 
T 118    G   194                                                                 
A 119    A   195                                                                 
V 120    V   196                                                                 
K 121    Q   197                                                                 
L 122    Y   198                                                                 
I 123    S   199                                                                 
E 124    G   200                                                                 
G 125    G   201                                                                 
G 126    R   202                                                                 
Y 127    F   203                                                                 
I 128    T   204                                                                 
V 129    I   205                                                                 
E 130    P   206                                                                 
A 131    R   207                                                                 
A 132    G   208                                                                 
I 133    V   209                                                                 
K 134    G   210                                                                 
W 135    R   217                                                                 
K 136    P   218                                                                 
T 137    I   219                                                                 
I 138    M   220                                                                 
K 139    D   221                                                                 
P 140    N   222                                                                 
T 141    S   223                                                                 
P 142    G   224                                                                 
N 143    R   225                                                                 
T 144    V   226                                                                 
V 145    V   227                                                                 
I 146    A   228                                                                 
G 147    I   229                                                                 
F 148    V   230                                                                 
N 149    L   231                                                                 
I 150    G   232                                                                 
Q 151    G   233                                                                 
V 152    A   234                                                                 
N 153    D   235                                                                 
K 158    E   236                                                                 
G 159    G   237                                                                 
Q 160    T   238                                                                 
R 161    R   239                                                                 
V 162    T   240                                                                 
G 163    A   241                                                                 
I 164    V   244                                                                 
I 165    V   245                                                                 
S 166    T   246                                                                 
W 167    W   247                                                                 
S 168    N   248                                                                 
D 169    S   249                                                                 
P 170    K   250                                                                 
T 171    G   251                                                                 
N 172    K   252                                                                 
N 173    T   253                                                                 
S 174    I   254                                                                 
W 175    K   255                                                                 
R 176    P   258                                                                 
D 177    E   259                                                                 
P 178    G   260                                                                 
S 179    T   261                                                                 
K 180    E   262                                                                 
F 181    E   263                                                                 
G 182    W   264                                                                 
TER                                                                              
END                                                                              



