
PFRMAT AL                                                                        
TARGET T0095                                                                     
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  4                                                                         
PARENT 1CI1_A                                                                    
D 388    E    78                                                                 
H 389    V    79                                                                 
V 390    S    80                                                                 
S 391    L    81                                                                 
D 392    Q    82                                                                 
S 393    I    83                                                                 
F 394    L    84                                                                 
L 395    K    85                                                                 
E 396    D    86                                                                 
T 397    Y    87                                                                 
N 398    G    88                                                                 
V 399    I    89                                                                 
P 400    S    90                                                                 
L 401    W    91                                                                 
L 402    V    92                                                                 
V 403    V    93                                                                 
L 404    L    94                                                                 
I 405    G    95                                                                 
E 406    H    96                                                                 
A 407    S    97                                                                 
K 414    E    98                                                                 
E 415    R    99                                                                 
V 416    R   100                                                                 
K 417    L   101                                                                 
E 418    Y   102                                                                 
Y 419    Y   103                                                                 
A 420    G   104                                                                 
Q 421    E   105                                                                 
V 422    T   106                                                                 
F 423    N   107                                                                 
R 424    E   108                                                                 
E 425    I   109                                                                 
H 426    V   110                                                                 
A 427    A   111                                                                 
N 428    E   112                                                                 
K 429    K   113                                                                 
L 430    V   114                                                                 
I 431    A   115                                                                 
E 432    Q   116                                                                 
V 433    A   117                                                                 
A 434    C   118                                                                 
N 435    A   119                                                                 
L 436    V   124                                                                 
A 437    I   125                                                                 
C 438    V   126                                                                 
S 439    C   127                                                                 
I 440    V   128                                                                 
S 441    G   129                                                                 
N 442    E   130                                                                 
N 443    T   131                                                                 
E 444    N   132                                                                 
E 445    E   133                                                                 
G 446    E   134                                                                 
V 447    R   135                                                                 
K 448    E   136                                                                 
L 449    A   137                                                                 
V 450    G   138                                                                 
R 451    R   139                                                                 
M 452    T   140                                                                 
S 453    A   141                                                                 
A 454    A   142                                                                 
S 455    V   143                                                                 
Q 456    V   144                                                                 
L 457    L   145                                                                 
A 467    T   146                                                                 
A 468    Q   147                                                                 
L 469    L   148                                                                 
A 470    A   149                                                                 
L 471    A   150                                                                 
A 472    V   151                                                                 
A 473    A   152                                                                 
K 474    Q   153                                                                 
P 475    K   154                                                                 
L 486    L   155                                                                 
F 487    S   156                                                                 
K 488    K   157                                                                 
E 489    E   158                                                                 
Q 490    A   159                                                                 
W 491    W   160                                                                 
E 492    S   161                                                                 
K 493    R   162                                                                 
Q 494    V   163                                                                 
V 495    V   164                                                                 
R 496    I   165                                                                 
V 497    A   166                                                                 
L 498    Y   167                                                                 
D 509    E   168                                                                 
D 510    P   169                                                                 
F 511    V   170                                                                 
L 512    W   171                                                                 
A 513    A   172                                                                 
V 514    I   173                                                                 
S 515    G   174                                                                 
E 516    T   175                                                                 
N 517    G   176                                                                 
H 518    K   177                                                                 
I 519    V   178                                                                 
L 520    A   179                                                                 
E 521    T   180                                                                 
D 522    Q   183                                                                 
V 523    A   184                                                                 
N 524    Q   185                                                                 
K 525    E   186                                                                 
C 526    V   187                                                                 
V 527    H   188                                                                 
I 528    E   189                                                                 
A 529    L   190                                                                 
L 530    L   191                                                                 
Q 531    R   192                                                                 
E 532    R   193                                                                 
K 533    W   194                                                                 
D 534    S   197                                                                 
V 535    K   198                                                                 
D 536    L   199                                                                 
G 537    G   200                                                                 
L 538    T   201                                                                 
D 539    D   202                                                                 
R 540    I   203                                                                 
T 541    A   204                                                                 
A 542    A   205                                                                 
G 543    G   213                                                                 
A 544    S   214                                                                 
I 545    V   215                                                                 
R 546    T   216                                                                 
G 547    A   217                                                                 
R 548    K   218                                                                 
A 549    N   219                                                                 
A 550    A   220                                                                 
R 551    R   221                                                                 
V 552    T   222                                                                 
I 553    L   223                                                                 
H 554    G   231                                                                 
V 555    F   232                                                                 
V 556    L   233                                                                 
T 557    V   234                                                                 
S 558    G   235                                                                 
E 559    G   236                                                                 
M 560    A   237                                                                 
D 561    S   238                                                                 
E 564    L   239                                                                 
P 565    K   240                                                                 
G 566    P   241                                                                 
V 567    E   242                                                                 
Y 568    F   243                                                                 
T 569    V   244                                                                 
K 571    E   245                                                                 
V 572    I   246                                                                 
L 573    I   247                                                                 
E 574    E   248                                                                 
A 575    A   249                                                                 
T 576    T   250                                                                 
K 577    K   251                                                                 
TER                                                                              
END                                                                              


                          Ralf Zimmer
  LLL    LL   LL  LLLL    German Nat.Res.Center for Information Technology
 L       L L L L  L   L   Schloss Birlinghoven, D-53754 Sankt Augustin
L  LLL   L  L  L  L    L  Tel: +49-2241-14-2818, Fax: +49-2241-14-2656
 L   L   L     L  L   L   Email: Ralf.Zimmer@gmd.de
  LLL    L     L  LLLL    WWW: http://www.gmd.de/SCAI/people/zimmer.html




