
PFRMAT AL                                                                        
TARGET T0124                                                                     
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  3                                                                         
PARENT 1AII                                                                      
N 880    H    80                                                                 
M 881    F    81                                                                 
K 882    E    82                                                                 
E 883    H    83                                                                 
V 884    M    85                                                                 
T 885    V    86                                                                 
Q 886    A    87                                                                 
L 887    L    88                                                                 
P 888    V    89                                                                 
E 889    T    90                                                                 
P 890    P    91                                                                 
Q 891    P    92                                                                 
S 894    A    93                                                                 
L 895    V    94                                                                 
A 896    F    95                                                                 
E 897    D    96                                                                 
L 898    A    97                                                                 
Q 899    K    98                                                                 
Q 900    Q    99                                                                 
M 901    L   100                                                                 
K 902    K   101                                                                 
L 903    K   102                                                                 
F 904    S   103                                                                 
L 905    M   104                                                                 
K 906    K   105                                                                 
L 907    G   106                                                                 
L 908    A   107                                                                 
K 909    G   108                                                                 
K 910    T   109                                                                 
Q 911    N   110                                                                 
E 912    E   111                                                                 
K 913    D   112                                                                 
E 914    A   113                                                                 
L 915    L   114                                                                 
K 916    I   115                                                                 
E 917    E   116                                                                 
L 918    L   118                                                                 
E 919    T   119                                                                 
R 920    T   120                                                                 
K 921    R   121                                                                 
G 922    T   122                                                                 
S 923    S   123                                                                 
K 924    R   124                                                                 
R 925    Q   125                                                                 
R 926    M   126                                                                 
E 927    K   127                                                                 
E 928    D   128                                                                 
L 929    I   129                                                                 
L 930    S   130                                                                 
Q 931    Q   131                                                                 
K 932    A   132                                                                 
Y 933    Y   133                                                                 
S 934    Y   134                                                                 
V 935    T   135                                                                 
V 941    V   136                                                                 
Y 942    Y   137                                                                 
P 943    K   138                                                                 
R 944    K   139                                                                 
G 945    S   140                                                                 
L 979    L   141                                                                 
D 980    G   142                                                                 
S 981    D   143                                                                 
Q 982    D   144                                                                 
V 983    I   145                                                                 
V 984    S   146                                                                 
E 985    S   147                                                                 
L 986    T   149                                                                 
K 987    S   150                                                                 
E 988    G   151                                                                 
R 989    D   152                                                                 
L 990    F   153                                                                 
E 991    R   154                                                                 
M 992    K   155                                                                 
E 993    A   156                                                                 
L 994    L   157                                                                 
I 995    L   158                                                                 
H 996    T   159                                                                 
L 997    L   160                                                                 
G 998    A   161                                                                 
E 999    D   162                                                                 
E 1000    G   163                                                                 
Y 1001    R   164                                                                 
H 1002    R   165                                                                 
D 1003    D   166                                                                 
G 1004    E   167                                                                 
I 1005    S   168                                                                 
R 1006    L   169                                                                 
R 1007    K   170                                                                 
R 1008    V   171                                                                 
K 1009    D   172                                                                 
E 1010    E   173                                                                 
Q 1011    H   174                                                                 
H 1012    L   175                                                                 
A 1013    A   176                                                                 
T 1014    K   177                                                                 
E 1015    Q   178                                                                 
Q 1016    D   179                                                                 
T 1017    A   180                                                                 
A 1018    D   196                                                                 
K 1019    K   197                                                                 
I 1020    F   198                                                                 
T 1021    T   199                                                                 
E 1022    E   200                                                                 
L 1023    I   201                                                                 
A 1024    L   202                                                                 
R 1025    C   203                                                                 
E 1026    L   204                                                                 
K 1027    R   205                                                                 
Q 1028    S   206                                                                 
I 1029    F   207                                                                 
A 1030    P   208                                                                 
E 1031    Q   209                                                                 
L 1032    L   210                                                                 
K 1033    K   211                                                                 
A 1034    L   212                                                                 
L 1035    Y   217                                                                 
K 1036    R   218                                                                 
E 1037    N   219                                                                 
S 1038    I   220                                                                 
S 1039    S   221                                                                 
E 1040    Q   222                                                                 
S 1041    K   223                                                                 
N 1042    D   224                                                                 
I 1043    I   225                                                                 
K 1044    D   227                                                                 
D 1045    S   228                                                                 
I 1046    I   229                                                                 
K 1047    K   230                                                                 
K 1048    G   231                                                                 
K 1049    E   232                                                                 
L 1050    L   233                                                                 
E 1051    S   234                                                                 
A 1052    G   235                                                                 
K 1053    H   236                                                                 
R 1054    F   237                                                                 
L 1055    E   238                                                                 
D 1056    D   239                                                                 
R 1057    L   240                                                                 
I 1058    L   241                                                                 
Q 1059    L   242                                                                 
V 1060    A   243                                                                 
M 1061    I   244                                                                 
M 1062    V   245                                                                 
R 1063    N   246                                                                 
S 1064    C   247                                                                 
T 1065    V   248                                                                 
S 1066    R   249                                                                 
D 1067    N   250                                                                 
K 1068    T   251                                                                 
A 1069    P   252                                                                 
A 1070    L   255                                                                 
Q 1071    A   256                                                                 
E 1072    E   257                                                                 
R 1073    R   258                                                                 
L 1074    L   259                                                                 
K 1075    H   260                                                                 
K 1076    R   261                                                                 
E 1077    A   262                                                                 
I 1078    L   263                                                                 
N 1079    K   264                                                                 
N 1080    G   265                                                                 
S 1081    I   266                                                                 
H 1082    G   267                                                                 
I 1083    T   268                                                                 
Q 1084    D   269                                                                 
E 1085    E   270                                                                 
V 1086    F   271                                                                 
V 1087    T   272                                                                 
T 1089    L   273                                                                 
I 1090    N   274                                                                 
K 1091    R   275                                                                 
L 1092    I   276                                                                 
L 1093    M   277                                                                 
T 1094    V   278                                                                 
E 1095    S   279                                                                 
K 1096    R   280                                                                 
Y 1100    S   281                                                                 
Q 1101    E   282                                                                 
Q 1102    I   283                                                                 
K 1103    D   284                                                                 
L 1104    L   285                                                                 
E 1105    L   286                                                                 
E 1106    D   287                                                                 
K 1107    I   288                                                                 
Q 1108    R   289                                                                 
A 1109    T   290                                                                 
E 1110    E   291                                                                 
N 1111    F   292                                                                 
L 1112    K   293                                                                 
R 1113    K   294                                                                 
A 1114    H   295                                                                 
I 1115    Y   296                                                                 
Q 1116    G   297                                                                 
E 1117    Y   298                                                                 
K 1118    S   299                                                                 
E 1119    Y   301                                                                 
G 1120    S   302                                                                 
Q 1121    A   303                                                                 
L 1122    I   304                                                                 
Q 1123    K   305                                                                 
Q 1124    S   306                                                                 
E 1125    D   307                                                                 
A 1126    T   308                                                                 
V 1127    S   309                                                                 
A 1128    G   310                                                                 
E 1129    D   311                                                                 
Y 1130    Y   312                                                                 
E 1131    E   313                                                                 
E 1132    I   314                                                                 
K 1133    T   315                                                                 
L 1134    L   316                                                                 
K 1135    L   317                                                                 
T 1136    K   318                                                                 
L 1137    I   319                                                                 
V 1139    C   320                                                                 
E 1140    G   321                                                                 
V 1141    G   322                                                                 
Q 1142    D   323                                                                 
E 1143    D   324                                                                 
TER                                                                              
END                                                                              



