
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  2                                                                         
PARENT 2A0B                                                                      
S 393    S   657                                                                 
F 394    K   658                                                                 
L 395    S   659                                                                 
E 396    E   660                                                                 
T 397    A   661                                                                 
N 398    L   662                                                                 
V 399    L   663                                                                 
P 400    D   664                                                                 
L 401    I   665                                                                 
L 402    P   666                                                                 
V 403    M   667                                                                 
L 404    L   668                                                                 
I 405    E   669                                                                 
E 406    Q   670                                                                 
A 407    Y   671                                                                 
A 408    L   672                                                                 
K 409    E   673                                                                 
N 410    L   674                                                                 
G 411    V   675                                                                 
N 412    G   676                                                                 
E 413    P   677                                                                 
K 414    K   678                                                                 
E 415    L   679                                                                 
V 416    I   680                                                                 
K 417    T   681                                                                 
E 418    D   682                                                                 
Y 419    G   683                                                                 
A 420    L   684                                                                 
Q 421    A   685                                                                 
V 422    V   686                                                                 
F 423    F   687                                                                 
R 424    E   688                                                                 
E 425    K   689                                                                 
H 426    M   690                                                                 
A 427    M   691                                                                 
N 428    P   692                                                                 
K 429    G   693                                                                 
L 430    Y   694                                                                 
I 431    V   695                                                                 
E 432    S   696                                                                 
V 433    V   697                                                                 
A 434    L   698                                                                 
N 435    E   699                                                                 
L 436    S   700                                                                 
A 437    N   701                                                                 
C 438    L   702                                                                 
S 439    T   703                                                                 
I 440    A   704                                                                 
S 441    Q   705                                                                 
N 442    D   706                                                                 
N 443    K   707                                                                 
E 444    K   708                                                                 
E 445    G   709                                                                 
G 446    I   710                                                                 
V 447    V   711                                                                 
K 448    E   712                                                                 
L 449    E   713                                                                 
V 450    G   714                                                                 
R 451    H   715                                                                 
M 452    K   716                                                                 
S 453    I   717                                                                 
A 454    K   718                                                                 
S 455    G   719                                                                 
Q 456    A   720                                                                 
L 457    A   721                                                                 
E 458    G   722                                                                 
A 459    S   723                                                                 
L 460    V   724                                                                 
C 461    G   725                                                                 
P 462    L   726                                                                 
Q 463    R   727                                                                 
V 464    H   728                                                                 
I 465    L   729                                                                 
N 466    Q   730                                                                 
A 467    Q   731                                                                 
A 468    L   732                                                                 
L 469    G   733                                                                 
A 470    Q   734                                                                 
L 471    Q   735                                                                 
A 472    I   736                                                                 
A 473    Q   737                                                                 
K 474    S   738                                                                 
P 475    P   739                                                                 
Q 476    W   744                                                                 
S 477    E   745                                                                 
K 478    D   746                                                                 
L 479    N   747                                                                 
A 480    V   748                                                                 
Q 481    G   749                                                                 
E 482    E   750                                                                 
N 483    W   751                                                                 
M 484    I   752                                                                 
D 485    E   753                                                                 
L 486    E   754                                                                 
F 487    M   755                                                                 
K 488    K   756                                                                 
E 489    E   757                                                                 
Q 490    E   758                                                                 
W 491    W   759                                                                 
E 492    R   760                                                                 
K 493    H   761                                                                 
Q 494    D   762                                                                 
V 495    V   763                                                                 
R 496    E   764                                                                 
V 497    V   765                                                                 
L 498    L   766                                                                 
T 499    K   767                                                                 
D 500    A   768                                                                 
A 501    W   769                                                                 
V 502    V   770                                                                 
D 503    A   771                                                                 
D 504    K   772                                                                 
I 505    A   773                                                                 
T 506    T   774                                                                 
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




