PFRMAT AL 
TARGET T0054 
AUTHOR 4798-1984-8383 
REMARK CASP-3 target T0054, VanX, Enterococcus faecium 
REMARK 
METHOD This prediction is based, in part, on a threading algorithm described in 
METHOD three publications: 
METHOD (i) "A polynomial-time algorithm for a class of protein threading 
METHOD problems", by Ying Xu and Edward C. Uberbacher, CABIOS (journal) 
METHOD Vol.12, No.6, 1996 pp.511-517. 
METHOD (ii) "A New Method for Modeling and Solving the Protein Fold Recognition 
METHOD Problem", by Y. Xu, D. Xu, and E.C. Uberbacher, Proc. of RECOMB 98 
METHOD Second Annual Int'l Conf. on Computational Molecular Biology 
METHOD March 22-25, 1998, NEW York, NY, ACM Press, pp. 285-292. 
METHOD (iii) "An Efficient Computational Method for Globally Optimal Threading", 
METHOD by Y. Xu, D. Xu, and E.C. Uberbacher, invited paper to appear in 
METHOD Journal of Computational Biology, 1998. 
METHOD 
METHOD 
METHOD The prediction is also based, in part, on a different threading algorithm 
METHOD described in the following publication: 
METHOD (iv) "A fast, reliable method for threading", by O.H. Crawford, submitted 
METHOD to Bioinformatics (journal) 
METHOD 
METHOD 
METHOD The energy model employed in the threading is based on improvements and 
METHOD extensions of the energy modeling described in Refs. (ii) and (iii) 
METHOD and in the following paper: 
METHOD (v) "Protein Fold Recognition at the Secondary Structure Level", 
METHOD by D. Xu, M.A. Unseren, Y. Xu, and E.C. Uberbacher, Submitted. 
METHOD 
METHOD Refinement was carried out using MODELLER (A. Sali and T. L. Blundell. 
METHOD Comparative protein modelling by satisfaction of spatial restraints. 
METHOD J. Mol. Biol. 234, 779-815,1993.). 
METHOD 
METHOD The last column (temperature factor field) does NOT correspond 
METHOD to the error estimates in this prediction. The confidence level 
METHOD is high for the structures around the active sites centered at 
METHOD the zinc atom. 
METHOD 
METHOD Members of Oak Ridge National Laboratory's Computational Biosciences 
METHOD Section participating in CASP3  include (in alphabetical order): 
METHOD Oakley Crawford, J. Ralph Einstein, Frank W. Larimer, Richard Mural, 
METHOD Edward C. Uberbacher, Michael A. Unseren, Dong Xu, Ying Xu, and Ge Zhang 
MODEL  2  
PARENT 2glt 
I      3  V     82  
G      4  I     83  
F      5  L     84  
T      6  M     85  
D      9  T     93  
E     10  E     94  
I     11  F     95  
V     12  I     96  
H     13  Y     97  
G     14  A     98  
V     15  T     99  
R     16  Y    100  
W     17  I    101  
D     18  L    102  
A     19  E    103  
K     20  R    104  
Y     21  A    105  
A     22  E    106  
T     23  E    107  
R     39  L    111  
I     40  I    112  
V     41  V    113  
A     47  P    116  
E     48  Q    117  
S     49  S    118  
L     50  L    119  
L     51  R    120  
K     52  D    121  
A     53  C    122 
K     54  N    123 
G     63  T    138  
L     64  L    139  
L     65  V    140  
L     66  T    141  
K     73  K    144  
R     74  A    145  
A     75  Q    146  
V     76  L    147  
N     77  K    148  
C     78  A    149  
F     79  F    150  
M     80  W    151  
Q     81  E    152  
W     82  K    153  
A     83  H    154  
L     90  I    157  
T     91  I    158  
K     92  L    159  
E     93  K    160  
S     94  P    161  
Y     96  L    180  
P     97  G    181  
N     98  V    182  
I     99  I    183  
D    100  A    184  
R    101  E    185  
T    102  T    186  
E    103  L    187  
Y    109  C    195  
V    110  M    196  
A    111  A    197  
S    112  Q    198  
K    113  N    199  
H    116  D    208  
S    117  K    209  
R    118  R    210  
G    119  V    211  
S    120  L    212  
A    121  V    213  
I    122  V    214  
D    130  Y    221  
T    131  C    222  
G    132  L    223  
E    133  A    224  
R    147  E    243  
S    148  P    244  
H    149  R    245  
H    150  P    246  
S    156  E    249  
C    157  S    250  
N    158  D    251  
E    159  W    252  
A    160  K    253  
Q    161  I    254  
N    162  A    255  
R    163  R    256  
R    164  Q    257  
R    165  I    258  
L    166  G    259  
R    167  P    260  
S    168  T    261  
I    169  L    262  
M    170  K    263  
E    171  E    264  
V    186  F    269  
L    187  V    270  
R    188  G    271  
D    189  L    272  
E    190  D    273  
P    191  I    274  
Y    192  I    275  
TER 
END 
