
PFRMAT AL                                                                        
TARGET T0088                                                                     
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                                                                      
A   1    P   139                                                                 
V   2    L   140                                                                 
S   3    H   141                                                                 
F   4    V   142                                                                 
I   5    K   143                                                                 
G   6    G   144                                                                 
S   7    T   145                                                                 
T   8    I   146                                                                 
E   9    D   147                                                                 
N  10    H   148                                                                 
D  11    P   149                                                                 
V  12    V   150                                                                 
G  13    L   151                                                                 
P  14    S   152                                                                 
Q  16    K   153                                                                 
G  17    L   154                                                                 
S  18    K   155                                                                 
Y  19    F   156                                                                 
S  20    T   157                                                                 
S  21    K   158                                                                 
T  22    S   159                                                                 
H  23    S   160                                                                 
A  24    A   161                                                                 
M  25    M   173                                                                 
D  26    R   174                                                                 
N  27    S   175                                                                 
L  28    E   176                                                                 
P  29    A   177                                                                 
F  30    F   178                                                                 
V  31    T   179                                                                 
Y  32    Y   180                                                                 
N  33    T   181                                                                 
T  34    S   182                                                                 
G  35    E   183                                                                 
Y  36    H   184                                                                 
N  37    P   185                                                                 
I  38    E   186                                                                 
G  39    G   187                                                                 
Y  40    W   191                                                                 
Q  41    H   192                                                                 
N  42    H   193                                                                 
A  43    G   194                                                                 
N  44    A   195                                                                 
V  45    V   196                                                                 
W  46    Q   197                                                                 
R  47    Y   198                                                                 
I  48    S   199                                                                 
S  49    G   200                                                                 
G  50    G   201                                                                 
G  51    R   202                                                                 
F  52    F   203                                                                 
C  53    T   204                                                                 
V  54    I   205                                                                 
G  55    P   206                                                                 
L  56    N   222                                                                 
D  57    S   223                                                                 
G  58    G   224                                                                 
K  59    R   225                                                                 
V  60    V   226                                                                 
D  61    V   227                                                                 
L  62    A   228                                                                 
P  63    I   229                                                                 
V  64    V   230                                                                 
V  65    L   231                                                                 
G  66    G   232                                                                 
S  67    G   233                                                                 
L  68    A   234                                                                 
D  69    D   235                                                                 
G  70    E   236                                                                 
Q  71    G   237                                                                 
S  72    T   238                                                                 
I  73    R   239                                                                 
Y  74    T   240                                                                 
G  75    A   241                                                                 
V  80    L   242                                                                 
G  81    S   243                                                                 
L  82    V   244                                                                 
L  83    V   245                                                                 
I  84    T   246                                                                 
W  85    W   247                                                                 
M  86    N   248                                                                 
G  87    S   249                                                                 
D  88    K   250                                                                 
T  89    G   251                                                                 
N  90    K   252                                                                 
Y  91    T   253                                                                 
S  92    I   254                                                                 
R  93    K   255                                                                 
G  94    T   256                                                                 
T  95    T   257                                                                 
A  96    P   258                                                                 
M  97    E   259                                                                 
S  98    G   260                                                                 
G  99    T   261                                                                 
N 100    E   262                                                                 
S 101    E   263                                                                 
W 102    W   264                                                                 
TER                                                                              
END                                                                              



