
PFRMAT AL                                                                        
TARGET T0108                                                                     
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 1ULO                                                                      
D  54    A     1                                                                 
S  55    S     2                                                                 
P  56    P     3                                                                 
I  57    I     4                                                                 
T  58    G     5                                                                 
A  59    E     6                                                                 
I  60    G     7                                                                 
N  61    T     8                                                                 
V  62    F     9                                                                 
E  63    D    10                                                                 
N  64    D    11                                                                 
A  65    G    12                                                                 
N  66    P    13                                                                 
N  67    E    14                                                                 
A  68    G    15                                                                 
L  69    W    16                                                                 
K  70    V    17                                                                 
I  71    A    18                                                                 
S  72    Y    19                                                                 
N  73    G    20                                                                 
L  74    T    21                                                                 
K  77    D    22                                                                 
G  78    G    23                                                                 
S  79    P    24                                                                 
N  80    L    25                                                                 
D  81    D    26                                                                 
L  82    T    27                                                                 
S  83    S    28                                                                 
E  84    T    29                                                                 
G  85    G    30                                                                 
N  86    A    31                                                                 
F  87    L    32                                                                 
W  88    C    33                                                                 
A  89    V    34                                                                 
N  90    A    35                                                                 
V  91    V    36                                                                 
R  92    P    37                                                                 
I  93    A    38                                                                 
S  94    G    39                                                                 
A  95    S    40                                                                 
D  96    A    41                                                                 
I  97    Q    42                                                                 
W  98    Y    43                                                                 
G  99    L    49                                                                 
Q 100    N    50                                                                 
S 101    G    51                                                                 
I 102    V    52                                                                 
N 103    A    53                                                                 
I 104    I    54                                                                 
Y 105    E    55                                                                 
G 106    E    56                                                                 
D 107    G    57                                                                 
T 108    T    58                                                                 
K 109    T    59                                                                 
L 110    Y    60                                                                 
T 111    T    61                                                                 
M 112    L    62                                                                 
D 113    R    63                                                                 
V 114    Y    64                                                                 
I 115    T    65                                                                 
A 116    A    66                                                                 
P 117    T    67                                                                 
T 118    A    68                                                                 
P 119    S    69                                                                 
V 120    T    70                                                                 
N 121    D    71                                                                 
V 122    V    72                                                                 
S 123    T    73                                                                 
I 124    V    74                                                                 
A 125    R    75                                                                 
N 148    A    76                                                                 
F 149    L    77                                                                 
V 150    V    78                                                                 
A 151    G    79                                                                 
Q 152    Q    80                                                                 
T 153    N    81                                                                 
D 154    G    82                                                                 
G 155    A    83                                                                 
T 156    P    84                                                                 
Y 157    Y    85                                                                 
K 158    G    86                                                                 
A 159    T    87                                                                 
T 160    V    88                                                                 
L 161    L    89                                                                 
T 162    D    90                                                                 
I 163    T    91                                                                 
S 164    S    92                                                                 
T 165    P    93                                                                 
N 166    A    94                                                                 
D 167    L    95                                                                 
S 168    T   103                                                                 
P 169    E   104                                                                 
N 170    T   105                                                                 
F 171    F   106                                                                 
N 172    T   107                                                                 
T 173    A   108                                                                 
I 174    S   109                                                                 
A 175    A   110                                                                 
T 176    T   111                                                                 
D 177    P   116                                                                 
A 178    A   117                                                                 
A 179    A   118                                                                 
D 180    D   119                                                                 
S 181    D   120                                                                 
V 182    P   121                                                                 
V 183    E   122                                                                 
T 184    G   123                                                                 
N 185    Q   124                                                                 
M 186    I   125                                                                 
I 187    A   126                                                                 
L 188    F   127                                                                 
F 189    Q   128                                                                 
V 190    L   129                                                                 
G 191    G   130                                                                 
S 192    G   131                                                                 
N 193    F   132                                                                 
S 194    S   133                                                                 
D 195    A   134                                                                 
N 196    T   138                                                                 
I 197    L   139                                                                 
S 198    C   140                                                                 
L 199    L   141                                                                 
D 200    D   142                                                                 
N 201    D   143                                                                 
I 202    V   144                                                                 
K 203    A   145                                                                 
F 204    L   146                                                                 
T 205    D   147                                                                 
K 206    S   148                                                                 
TER                                                                              
END                                                                              



