
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  2                                                                         
PARENT 1QUU_A                                                                    
A 896    E   125                                                                 
E 897    T   126                                                                 
L 898    I   127                                                                 
Q 899    D   128                                                                 
Q 900    Q   129                                                                 
M 901    L   130                                                                 
K 902    H   131                                                                 
L 905    L   132                                                                 
K 906    E   133                                                                 
L 907    F   134                                                                 
L 908    A   135                                                                 
K 909    K   136                                                                 
K 910    R   137                                                                 
E 912    A   138                                                                 
K 913    A   139                                                                 
E 914    P   140                                                                 
L 915    F   141                                                                 
K 916    N   142                                                                 
E 917    N   143                                                                 
L 918    W   144                                                                 
R 926    M   145                                                                 
E 927    E   146                                                                 
E 928    G   147                                                                 
L 929    A   148                                                                 
L 930    M   149                                                                 
Q 931    E   150                                                                 
K 932    D   151                                                                 
Y 933    L   152                                                                 
S 934    Q   153                                                                 
V 935    D   154                                                                 
L 936    M   155                                                                 
F 937    F   156                                                                 
L 938    I   157                                                                 
E 939    V   158                                                                 
P 940    H   159                                                                 
L 986    S   160                                                                 
K 987    I   161                                                                 
E 988    E   162                                                                 
R 989    E   163                                                                 
L 990    I   164                                                                 
E 991    Q   165                                                                 
M 992    S   166                                                                 
L 994    L   167                                                                 
I 995    I   168                                                                 
H 996    T   169                                                                 
L 997    A   170                                                                 
G 998    H   171                                                                 
E 999    E   172                                                                 
E 1000    Q   173                                                                 
Y 1001    F   174                                                                 
H 1002    K   175                                                                 
D 1003    A   176                                                                 
G 1004    T   177                                                                 
R 1008    L   178                                                                 
K 1009    P   179                                                                 
E 1010    E   180                                                                 
Q 1011    A   181                                                                 
H 1012    D   182                                                                 
A 1013    G   183                                                                 
T 1014    E   184                                                                 
E 1015    R   185                                                                 
Q 1016    Q   186                                                                 
T 1017    S   187                                                                 
A 1018    I   188                                                                 
K 1019    M   189                                                                 
I 1020    A   190                                                                 
T 1021    I   191                                                                 
E 1022    Q   192                                                                 
L 1023    N   193                                                                 
A 1024    E   194                                                                 
R 1025    V   195                                                                 
E 1026    E   196                                                                 
K 1027    K   197                                                                 
Q 1028    V   198                                                                 
I 1029    I   199                                                                 
A 1030    Q   200                                                                 
E 1031    S   201                                                                 
K 1033    Y   202                                                                 
A 1034    N   203                                                                 
L 1035    I   204                                                                 
K 1036    R   205                                                                 
E 1037    I   206                                                                 
S 1038    S   207                                                                 
S 1039    S   208                                                                 
E 1040    S   209                                                                 
S 1041    N   210                                                                 
N 1042    P   211                                                                 
I 1043    Y   212                                                                 
K 1044    S   213                                                                 
D 1045    T   214                                                                 
I 1046    V   215                                                                 
K 1047    T   216                                                                 
K 1048    D   218                                                                 
K 1049    E   219                                                                 
L 1050    L   220                                                                 
E 1051    R   221                                                                 
A 1052    T   222                                                                 
K 1053    K   223                                                                 
L 1055    W   224                                                                 
D 1056    D   225                                                                 
R 1057    K   226                                                                 
I 1058    V   227                                                                 
Q 1059    K   228                                                                 
V 1060    Q   229                                                                 
M 1061    L   230                                                                 
M 1062    V   231                                                                 
S 1064    P   232                                                                 
T 1065    I   233                                                                 
S 1066    R   234                                                                 
D 1067    D   235                                                                 
K 1068    Q   236                                                                 
A 1069    S   237                                                                 
A 1070    L   238                                                                 
Q 1071    Q   239                                                                 
E 1072    E   240                                                                 
R 1073    E   241                                                                 
L 1074    L   242                                                                 
K 1075    A   243                                                                 
K 1076    R   244                                                                 
E 1077    Q   245                                                                 
I 1078    H   246                                                                 
N 1079    A   247                                                                 
N 1080    N   248                                                                 
TER                                                                              
END                                                                              



