
PFRMAT AL                                                                        
TARGET T0101                                                                     
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 1RMG                                                                      
A  26    S     3                                                                 
D  27    G     4                                                                 
C  28    S     5                                                                 
S  29    V     6                                                                 
S  30    G     7                                                                 
D  31    P     8                                                                 
L  32    L     9                                                                 
T  33    T    10                                                                 
S  34    S    11                                                                 
G  35    A    12                                                                 
I  36    S    13                                                                 
S  37    G    16                                                                 
T  38    A    17                                                                 
K  39    T    18                                                                 
R  40    K    19                                                                 
I  41    T    20                                                                 
Y  42    C    21                                                                 
Y  43    N    22                                                                 
V  44    I    23                                                                 
A  45    L    24                                                                 
P  46    S    25                                                                 
N  47    Y    26                                                                 
G  48    G    27                                                                 
N  49    A    28                                                                 
S  50    V    29                                                                 
S  51    A    30                                                                 
N  52    D    31                                                                 
N  53    N    32                                                                 
G  54    S    33                                                                 
S  55    T    34                                                                 
S  56    D    35                                                                 
F  57    V    36                                                                 
N  58    G    37                                                                 
A  59    P    38                                                                 
S  62    A    39                                                                 
F  63    I    40                                                                 
S  64    T    41                                                                 
A  65    S    42                                                                 
A  66    A    43                                                                 
M  67    W    44                                                                 
A  68    A    45                                                                 
A  69    A    46                                                                 
V  70    C    47                                                                 
N  71    K    48                                                                 
P  72    S    49                                                                 
G  73    G    50                                                                 
E  74    G    51                                                                 
L  75    L    52                                                                 
I  76    V    53                                                                 
L  77    Y    54                                                                 
L  78    I    55                                                                 
K  79    P    56                                                                 
P  80    S    57                                                                 
G  81    G    58                                                                 
T  82    N    59                                                                 
Y  83    Y    60                                                                 
T  84    A    61                                                                 
I  85    L    62                                                                 
P  86    N    63                                                                 
Y  87    Y    83                                                                 
T  88    R    84                                                                 
Q  89    T    85                                                                 
G  90    G    86                                                                 
K  91    T    87                                                                 
G  92    A    88                                                                 
N  93    S    89                                                                 
T  94    G    90                                                                 
I  95    N    91                                                                 
T  96    L   103                                                                 
F  97    F   104                                                                 
N  98    S   105                                                                 
K  99    S   106                                                                 
S 100    T   107                                                                 
G 101    S   108                                                                 
K 102    K   109                                                                 
D 103    G   110                                                                 
G 104    A   111                                                                 
A 105    V   112                                                                 
P 106    Q   113                                                                 
I 107    G   114                                                                 
Y 108    F   115                                                                 
V 109    G   116                                                                 
A 110    Y   117                                                                 
A 111    V   118                                                                 
A 112    Y   119                                                                 
N 113    L   145                                                                 
C 114    V   146                                                                 
G 115    D   147                                                                 
R 116    A   148                                                                 
A 117    P   149                                                                 
V 118    A   150                                                                 
F 119    F   151                                                                 
D 120    H   152                                                                 
F 121    F   153                                                                 
S 122    T   154                                                                 
F 123    M   155                                                                 
P 124    D   156                                                                 
D 125    S   184                                                                 
S 126    N   185                                                                 
Q 127    I   186                                                                 
W 128    W   187                                                                 
V 129    V   188                                                                 
Q 130    H   189                                                                 
A 131    D   190                                                                 
S 132    V   191                                                                 
Y 133    N   207                                                                 
G 134    N   208                                                                 
F 135    I   209                                                                 
Y 136    L   210                                                                 
V 137    V   211                                                                 
T 138    E   212                                                                 
G 139    S   213                                                                 
D 140    I   214                                                                 
Y 141    Y   215                                                                 
W 142    C   216                                                                 
Y 143    N   217                                                                 
F 144    W   218                                                                 
K 145    A   229                                                                 
G 146    D   230                                                                 
V 147    T   231                                                                 
E 148    D   232                                                                 
V 149    V   233                                                                 
T 150    T   234                                                                 
R 151    D   235                                                                 
A 152    I   236                                                                 
G 153    V   237                                                                 
Y 154    Y   238                                                                 
Q 155    R   239                                                                 
G 156    N   240                                                                 
A 157    V   241                                                                 
Y 158    Y   242                                                                 
V 159    T   243                                                                 
I 160    W   244                                                                 
G 161    S   245                                                                 
S 162    S   246                                                                 
H 163    N   247                                                                 
N 164    Q   248                                                                 
T 165    M   249                                                                 
F 166    Y   250                                                                 
E 167    M   251                                                                 
N 168    I   252                                                                 
T 169    K   253                                                                 
A 170    S   254                                                                 
F 171    N   255                                                                 
H 172    G   256                                                                 
H 173    G   257                                                                 
N 174    S   258                                                                 
R 175    G   259                                                                 
N 176    T   260                                                                 
T 177    V   261                                                                 
G 178    S   262                                                                 
L 179    N   263                                                                 
E 180    V   264                                                                 
I 181    I   270                                                                 
N 182    G   271                                                                 
N 183    H   272                                                                 
G 184    G   273                                                                 
G 185    N   274                                                                 
S 186    A   275                                                                 
Y 187    Y   276                                                                 
N 188    S   277                                                                 
T 189    L   278                                                                 
V 190    D   279                                                                 
A 208    I   280                                                                 
D 209    D   281                                                                 
G 210    G   282                                                                 
F 211    Y   283                                                                 
G 212    W   284                                                                 
P 213    S   285                                                                 
K 214    S   286                                                                 
Q 215    M   287                                                                 
K 216    T   288                                                                 
Q 217    A   289                                                                 
G 218    V   290                                                                 
S 232    A   291                                                                 
D 233    G   292                                                                 
D 234    D   293                                                                 
G 235    G   294                                                                 
F 236    V   295                                                                 
D 237    Q   296                                                                 
L 238    L   297                                                                 
F 239    T   314                                                                 
D 240    R   315                                                                 
S 241    P   316                                                                 
P 242    P   317                                                                 
Q 243    I   318                                                                 
K 244    R   319                                                                 
V 245    V   320                                                                 
V 246    V   321                                                                 
I 247    C   322                                                                 
E 248    S   323                                                                 
N 249    D   324                                                                 
S 250    T   325                                                                 
W 251    A   326                                                                 
A 252    P   327                                                                 
F 253    C   328                                                                 
R 254    T   329                                                                 
N 255    D   330                                                                 
G 256    D   335                                                                 
I 257    I   336                                                                 
N 258    A   337                                                                 
Y 259    I   338                                                                 
W 260    W   339                                                                 
N 261    T   340                                                                 
D 262    E   341                                                                 
S 263    S   342                                                                 
A 264    G   343                                                                 
F 265    S   344                                                                 
A 266    S   352                                                                 
G 267    A   353                                                                 
N 268    Y   354                                                                 
G 269    G   355                                                                 
N 270    S   356                                                                 
G 271    G   357                                                                 
F 272    Y   358                                                                 
K 273    C   359                                                                 
L 274    L   360                                                                 
G 275    K   361                                                                 
G 276    D   362                                                                 
N 277    S   363                                                                 
Q 278    S   364                                                                 
A 279    S   365                                                                 
V 280    H   366                                                                 
G 281    T   367                                                                 
N 282    S   368                                                                 
H 283    Y   369                                                                 
R 284    T   370                                                                 
I 285    T   371                                                                 
T 286    T   372                                                                 
R 287    S   373                                                                 
S 288    T   374                                                                 
V 289    V   375                                                                 
A 290    T   376                                                                 
F 291    A   377                                                                 
V 294    A   378                                                                 
S 295    P   379                                                                 
K 296    S   380                                                                 
G 297    G   381                                                                 
F 298    Y   382                                                                 
D 299    S   383                                                                 
Q 300    A   384                                                                 
N 301    T   385                                                                 
N 302    T   386                                                                 
N 303    M   387                                                                 
A 304    A   388                                                                 
G 305    A   389                                                                 
G 306    D   390                                                                 
V 307    L   391                                                                 
G 318    A   392                                                                 
I 319    T   393                                                                 
N 320    A   394                                                                 
Y 321    F   395                                                                 
G 322    G   396                                                                 
F 323    L   397                                                                 
G 324    T   398                                                                 
S 325    A   399                                                                 
N 326    S   400                                                                 
V 327    I   401                                                                 
Q 328    P   402                                                                 
S 329    T   405                                                                 
G 330    I   406                                                                 
Q 331    P   407                                                                 
K 332    T   408                                                                 
H 333    S   409                                                                 
Y 334    F   410                                                                 
F 335    Y   411                                                                 
R 336    P   412                                                                 
N 337    G   413                                                                 
N 338    L   414                                                                 
V 339    T   415                                                                 
S 340    P   416                                                                 
L 341    Y   417                                                                 
S 342    S   418                                                                 
A 343    A   419                                                                 
S 344    L   420                                                                 
V 345    A   421                                                                 
T 346    G   422                                                                 
TER                                                                              
END                                                                              



