
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  1                                                                         
PARENT 1BR4_E                                                                    
D 388    E   529                                                                 
H 389    R   530                                                                 
V 390    P   531                                                                 
S 391    T   532                                                                 
D 392    N   533                                                                 
N 398    P   534                                                                 
V 399    P   535                                                                 
P 400    G   536                                                                 
L 401    V   537                                                                 
L 402    L   538                                                                 
V 403    A   539                                                                 
L 404    L   540                                                                 
I 405    L   541                                                                 
E 406    D   542                                                                 
A 407    E   543                                                                 
A 408    E   544                                                                 
K 409    C   545                                                                 
N 410    W   546                                                                 
G 411    F   547                                                                 
N 412    P   548                                                                 
E 413    K   549                                                                 
K 414    A   550                                                                 
E 415    T   551                                                                 
V 416    D   552                                                                 
K 417    T   553                                                                 
E 418    S   554                                                                 
Y 419    F   555                                                                 
A 420    V   556                                                                 
Q 421    E   557                                                                 
V 422    K   558                                                                 
F 423    L   559                                                                 
R 424    I   560                                                                 
E 425    Q   561                                                                 
H 426    E   562                                                                 
A 427    Q   563                                                                 
N 428    H   566                                                                 
K 429    A   567                                                                 
L 430    K   568                                                                 
I 431    F   569                                                                 
E 432    Q   570                                                                 
V 433    K   571                                                                 
A 434    S   572                                                                 
S 439    K   573                                                                 
I 440    Q   574                                                                 
S 441    L   575                                                                 
N 442    K   576                                                                 
N 443    D   577                                                                 
E 444    K   578                                                                 
E 445    T   579                                                                 
G 446    E   580                                                                 
V 447    F   581                                                                 
K 448    C   582                                                                 
L 449    I   583                                                                 
V 450    L   584                                                                 
R 451    Y   592                                                                 
M 452    N   593                                                                 
S 453    A   594                                                                 
A 454    S   595                                                                 
S 455    A   596                                                                 
Q 456    W   597                                                                 
L 457    L   598                                                                 
E 458    T   599                                                                 
A 459    K   600                                                                 
L 460    N   601                                                                 
C 461    M   602                                                                 
P 462    D   603                                                                 
Q 463    P   604                                                                 
V 464    L   605                                                                 
I 465    N   606                                                                 
N 466    D   607                                                                 
A 467    N   608                                                                 
A 468    V   609                                                                 
L 469    T   610                                                                 
A 470    S   611                                                                 
L 471    L   612                                                                 
A 472    L   613                                                                 
A 473    N   614                                                                 
K 474    Q   615                                                                 
P 475    S   616                                                                 
Q 476    S   617                                                                 
S 477    D   618                                                                 
K 478    K   619                                                                 
L 479    F   620                                                                 
A 480    V   621                                                                 
Q 481    A   622                                                                 
E 482    D   623                                                                 
Q 490    L   624                                                                 
W 491    W   625                                                                 
E 492    K   626                                                                 
K 493    D   627                                                                 
Q 494    V   628                                                                 
V 495    D   629                                                                 
R 496    R   630                                                                 
V 497    I   631                                                                 
L 498    V   632                                                                 
T 499    G   633                                                                 
D 500    L   634                                                                 
N 524    F   656                                                                 
C 526    T   658                                                                 
V 527    V   659                                                                 
I 528    G   660                                                                 
A 529    Q   661                                                                 
L 530    L   662                                                                 
Q 531    Y   663                                                                 
E 532    K   664                                                                 
K 533    E   665                                                                 
G 537    Q   666                                                                 
L 538    L   667                                                                 
D 539    T   668                                                                 
R 540    K   669                                                                 
T 541    L   670                                                                 
A 542    M   671                                                                 
G 543    T   672                                                                 
A 544    T   673                                                                 
I 545    L   674                                                                 
R 546    R   675                                                                 
G 547    N   676                                                                 
A 550    T   677                                                                 
R 551    N   678                                                                 
V 552    P   679                                                                 
I 553    N   680                                                                 
H 554    F   681                                                                 
V 555    V   682                                                                 
V 556    R   683                                                                 
T 557    C   684                                                                 
S 558    I   685                                                                 
E 559    I   686                                                                 
M 560    P   687                                                                 
D 561    N   688                                                                 
N 562    E   690                                                                 
Y 563    K   691                                                                 
E 564    R   692                                                                 
P 565    A   693                                                                 
G 566    G   694                                                                 
V 567    K   695                                                                 
Y 568    L   696                                                                 
T 569    D   697                                                                 
E 570    A   698                                                                 
K 571    H   699                                                                 
V 572    L   700                                                                 
L 573    V   701                                                                 
A 575    L   702                                                                 
T 576    E   703                                                                 
K 577    Q   704                                                                 
L 578    L   705                                                                 
L 579    R   706                                                                 
S 580    C   707                                                                 
N 581    N   708                                                                 
Q 590    G   709                                                                 
V 591    V   710                                                                 
E 592    L   711                                                                 
A 593    E   712                                                                 
A 594    G   713                                                                 
V 595    I   714                                                                 
E 596    R   715                                                                 
A 597    I   716                                                                 
L 598    C   717                                                                 
S 599    R   718                                                                 
S 600    Q   719                                                                 
D 601    G   720                                                                 
P 602    F   721                                                                 
A 603    P   722                                                                 
Q 604    N   723                                                                 
P 605    R   724                                                                 
M 606    I   725                                                                 
D 607    V   726                                                                 
E 608    F   727                                                                 
N 609    Q   728                                                                 
E 610    E   729                                                                 
F 611    F   730                                                                 
I 612    R   731                                                                 
D 613    Q   732                                                                 
A 614    R   733                                                                 
S 615    Y   734                                                                 
R 616    E   735                                                                 
L 617    I   736                                                                 
V 618    L   737                                                                 
Y 619    A   738                                                                 
D 620    A   739                                                                 
G 621    N   740                                                                 
I 622    F   746                                                                 
R 623    M   747                                                                 
D 624    D   748                                                                 
I 625    G   749                                                                 
R 626    K   750                                                                 
K 627    Q   751                                                                 
A 628    A   752                                                                 
V 629    C   753                                                                 
L 630    I   754                                                                 
M 631    L   755                                                                 
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




