
PFRMAT AL                                                                        
TARGET T0127                                                                     
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 1C3Q_C                                                                    
M   1    K     8                                                                 
T   2    C     9                                                                 
T   3    L    10                                                                 
A   4    T    11                                                                 
V   5    A    12                                                                 
A   6    V    13                                                                 
R   7    R    14                                                                 
L   8    R    15                                                                 
Q   9    H    16                                                                 
P  10    S    17                                                                 
S  11    P    18                                                                 
F  23    L    19                                                                 
S  24    V    20                                                                 
A  25    H    21                                                                 
I  26    S    22                                                                 
V  27    I    23                                                                 
G  28    T    24                                                                 
Q  29    N    26                                                                 
E  30    V    27                                                                 
D  31    V    28                                                                 
M  32    T    29                                                                 
K  33    N    30                                                                 
L  34    F    31                                                                 
A  35    T    32                                                                 
L  36    A    33                                                                 
L  37    N    34                                                                 
L  38    G    35                                                                 
T  39    L    36                                                                 
A  40    L    37                                                                 
V  41    M    45                                                                 
D  42    A    46                                                                 
P  43    Y    47                                                                 
G  44    A    48                                                                 
I  45    K    49                                                                 
G  46    E    50                                                                 
G  47    G    60                                                                 
V  48    A    61                                                                 
L  49    L    62                                                                 
V  50    V    63                                                                 
F  51    L    64                                                                 
G  52    N    65                                                                 
D  53    I    66                                                                 
R  54    G    67                                                                 
G  55    T    68                                                                 
T  56    L    69                                                                 
G  57    S    70                                                                 
K  58    K    71                                                                 
S  59    E    72                                                                 
A  61    S    73                                                                 
V  62    V    74                                                                 
R  63    E    75                                                                 
A  64    A    76                                                                 
L  65    M    77                                                                 
A  66    I    78                                                                 
A  67    I    79                                                                 
L  68    A    80                                                                 
L  69    G    81                                                                 
P  70    K    82                                                                 
E  71    S    83                                                                 
I  72    A    84                                                                 
A  74    N    85                                                                 
V  75    E    86                                                                 
E  76    H    87                                                                 
G  77    G    88                                                                 
C  78    V    89                                                                 
P  79    P    90                                                                 
V  80    V    91                                                                 
S  81    G    97                                                                 
S  82    A    98                                                                 
P  83    G    99                                                                 
N  84    A   100                                                                 
V  85    T   101                                                                 
E  86    P   102                                                                 
M  87    F   103                                                                 
I  88    R   104                                                                 
P  89    T   105                                                                 
D  90    E   106                                                                 
W  91    S   107                                                                 
A  92    A   108                                                                 
T  93    R   109                                                                 
N  98    D   110                                                                 
V  99    I   111                                                                 
I 100    I   112                                                                 
R 101    R   113                                                                 
K 102    E   114                                                                 
P 103    R   116                                                                 
T 104    L   117                                                                 
P 105    A   118                                                                 
V 106    A   119                                                                 
V 107    I   120                                                                 
D 108    R   121                                                                 
V 119    G   122                                                                 
G 120    N   123                                                                 
A 121    A   124                                                                 
L 122    A   125                                                                 
D 123    E   126                                                                 
I 124    I   127                                                                 
E 125    A   128                                                                 
R 126    H   129                                                                 
A 127    T   130                                                                 
I 128    V   131                                                                 
S 129    G   132                                                                 
K 130    V   133                                                                 
G 131    T   134                                                                 
E 132    D   135                                                                 
K 133    W   136                                                                 
A 134    L   137                                                                 
F 135    I   138                                                                 
A 141    K   139                                                                 
R 142    G   140                                                                 
A 143    V   141                                                                 
N 144    D   142                                                                 
R 145    A   143                                                                 
G 146    G   144                                                                 
L 155    E   145                                                                 
L 156    G   146                                                                 
E 157    G   147                                                                 
D 158    G   148                                                                 
H 159    D   149                                                                 
I 160    I   150                                                                 
V 161    I   151                                                                 
D 162    R   152                                                                 
L 163    L   153                                                                 
L 164    A   154                                                                 
L 165    Q   155                                                                 
D 166    Q   156                                                                 
V 167    A   157                                                                 
A 168    A   158                                                                 
Q 169    Q   159                                                                 
S 170    K   160                                                                 
G 171    L   161                                                                 
E 172    N   162                                                                 
N 173    T   163                                                                 
V 174    V   164                                                                 
V 175    I   165                                                                 
E 176    A   166                                                                 
R 177    G   169                                                                 
D 178    E   170                                                                 
G 179    V   171                                                                 
L 180    D   172                                                                 
S 181    V   173                                                                 
I 182    I   174                                                                 
R 183    A   175                                                                 
H 184    D   176                                                                 
P 185    T   177                                                                 
A 186    S   178                                                                 
R 187    H   179                                                                 
F 188    V   180                                                                 
V 189    Y   181                                                                 
L 190    T   182                                                                 
V 191    L   183                                                                 
G 192    H   184                                                                 
S 193    N   185                                                                 
G 194    G   186                                                                 
P 203    H   187                                                                 
Q 204    K   188                                                                 
L 205    L   189                                                                 
L 206    L   190                                                                 
D 207    T   191                                                                 
R 208    K   192                                                                 
P 247    V   193                                                                 
K 248    T   194                                                                 
D 249    G   195                                                                 
M 250    A   196                                                                 
D 251    G   197                                                                 
I 256    C   198                                                                 
L 257    L   199                                                                 
E 258    L   200                                                                 
A 259    T   201                                                                 
R 260    S   202                                                                 
D 275    V   203                                                                 
C 276    V   204                                                                 
A 277    G   205                                                                 
A 278    A   206                                                                 
L 279    F   207                                                                 
C 280    C   208                                                                 
I 281    A   209                                                                 
A 282    V   210                                                                 
L 283    E   211                                                                 
G 284    E   212                                                                 
S 285    N   213                                                                 
D 286    P   214                                                                 
R 289    L   215                                                                 
G 290    F   216                                                                 
E 291    A   217                                                                 
L 292    A   218                                                                 
T 293    I   219                                                                 
L 294    A   220                                                                 
L 295    A   221                                                                 
R 296    I   222                                                                 
S 297    S   223                                                                 
A 298    S   224                                                                 
R 299    Y   225                                                                 
A 300    G   226                                                                 
L 301    V   227                                                                 
A 302    A   228                                                                 
A 303    A   229                                                                 
L 304    Q   230                                                                 
E 305    L   231                                                                 
G 306    A   232                                                                 
A 307    A   233                                                                 
T 308    Q   234                                                                 
A 309    Q   235                                                                 
V 310    T   236                                                                 
G 311    A   237                                                                 
R 312    D   238                                                                 
D 313    K   239                                                                 
H 314    G   240                                                                 
L 315    P   241                                                                 
K 316    G   242                                                                 
R 317    S   243                                                                 
V 318    F   244                                                                 
A 319    Q   245                                                                 
T 320    I   246                                                                 
A 322    E   247                                                                 
L 323    L   248                                                                 
S 324    L   249                                                                 
H 325    N   250                                                                 
R 326    K   251                                                                 
L 327    L   252                                                                 
R 328    S   253                                                                 
R 329    T   254                                                                 
D 330    V   255                                                                 
P 331    T   256                                                                 
L 332    E   257                                                                 
D 333    Q   258                                                                 
E 334    D   259                                                                 
A 335    V   260                                                                 
G 336    Q   261                                                                 
S 337    E   262                                                                 
V 341    W   263                                                                 
A 342    A   264                                                                 
R 343    T   265                                                                 
T 344    I   266                                                                 
V 345    E   267                                                                 
E 346    R   268                                                                 
E 347    V   269                                                                 
T 348    T   270                                                                 
L 349    V   271                                                                 
P 350    S   272                                                                 
TER                                                                              
END                                                                              



