REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0059AL009_2 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0059  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0059,  Sm D3 protein (the N-terminal 75 residues)  
REMARK  
METHOD This prediction is based, in part, on a threading algorithm described in  
METHOD three publications:  
METHOD (i) "An Efficient Computational Method for Globally Optimal Threading",  
METHOD by Y. Xu, D. Xu, and E.C. Uberbacher, Journal of Computational Biology,   
METHOD Vol. 5(3), pp. 609-626, 1998.  
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) "A polynomial-time algorithm for a class of protein threading  
METHOD problems", by Ying Xu and Edward C. Uberbacher, CABIOS, Vol. 12 (6),  
METHOD pp.511-517, 1996.  
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  
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 UNREFINED   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1f3g 
ATOM      1  N   ILE     3      34.798  33.076  32.181  1.00  0.00              
ATOM      2  CA  ILE     3      35.324  34.368  32.497  1.00  0.00              
ATOM      3  C   ILE     3      34.199  35.126  33.119  1.00  0.00              
ATOM      4  O   ILE     3      33.071  34.742  32.947  1.00  0.00              
ATOM      5  N   GLY     4      34.483  36.192  33.847  1.00  0.00              
ATOM      6  CA  GLY     4      33.381  36.940  34.430  1.00  0.00              
ATOM      7  C   GLY     4      33.987  37.934  35.387  1.00  0.00              
ATOM      8  O   GLY     4      35.116  38.346  35.231  1.00  0.00              
ATOM      9  N   VAL     5      33.230  38.292  36.389  1.00  0.00              
ATOM     10  CA  VAL     5      33.647  39.199  37.397  1.00  0.00              
ATOM     11  C   VAL     5      33.485  38.444  38.738  1.00  0.00              
ATOM     12  O   VAL     5      33.040  37.315  38.737  1.00  0.00              
ATOM     13  N   PRO     6      33.841  39.066  39.835  1.00  0.00              
ATOM     14  CA  PRO     6      33.670  38.532  41.146  1.00  0.00              
ATOM     15  C   PRO     6      33.080  39.700  41.910  1.00  0.00              
ATOM     16  O   PRO     6      33.373  40.853  41.562  1.00  0.00              
ATOM     17  N   ILE     7      32.274  39.440  42.945  1.00  0.00              
ATOM     18  CA  ILE     7      31.667  40.518  43.768  1.00  0.00              
ATOM     19  C   ILE     7      32.083  40.364  45.247  1.00  0.00              
ATOM     20  O   ILE     7      32.150  39.268  45.742  1.00  0.00              
ATOM     21  N   LYS     8      32.392  41.426  45.968  1.00  0.00              
ATOM     22  CA  LYS     8      32.714  41.286  47.406  1.00  0.00              
ATOM     23  C   LYS     8      31.362  41.610  47.969  1.00  0.00              
ATOM     24  O   LYS     8      30.921  42.747  47.854  1.00  0.00              
ATOM     25  N   VAL     9      30.665  40.669  48.559  1.00  0.00              
ATOM     26  CA  VAL     9      29.318  40.887  49.053  1.00  0.00              
ATOM     27  C   VAL     9      29.214  41.867  50.211  1.00  0.00              
ATOM     28  O   VAL     9      30.113  42.116  51.036  1.00  0.00              
ATOM     29  N   HIS    16      21.320  38.206  50.223  1.00  0.00              
ATOM     30  CA  HIS    16      20.628  37.258  49.360  1.00  0.00              
ATOM     31  C   HIS    16      21.342  37.100  47.997  1.00  0.00              
ATOM     32  O   HIS    16      21.965  38.032  47.513  1.00  0.00              
ATOM     33  N   ILE    17      21.270  35.933  47.417  1.00  0.00              
ATOM     34  CA  ILE    17      21.832  35.633  46.104  1.00  0.00              
ATOM     35  C   ILE    17      20.634  35.489  45.215  1.00  0.00              
ATOM     36  O   ILE    17      19.862  34.571  45.394  1.00  0.00              
ATOM     37  N   VAL    18      20.475  36.418  44.272  1.00  0.00              
ATOM     38  CA  VAL    18      19.313  36.492  43.380  1.00  0.00              
ATOM     39  C   VAL    18      19.538  36.049  41.933  1.00  0.00              
ATOM     40  O   VAL    18      20.670  35.911  41.479  1.00  0.00              
ATOM     41  N   THR    22      15.400  33.167  33.448  1.00  0.00              
ATOM     42  CA  THR    22      15.630  31.815  32.946  1.00  0.00              
ATOM     43  C   THR    22      15.250  30.693  33.901  1.00  0.00              
ATOM     44  O   THR    22      14.362  30.817  34.747  1.00  0.00              
ATOM     45  N   ASN    23      15.982  29.596  33.739  1.00  0.00              
ATOM     46  CA  ASN    23      15.794  28.389  34.483  1.00  0.00              
ATOM     47  C   ASN    23      16.973  27.952  35.322  1.00  0.00              
ATOM     48  O   ASN    23      18.049  27.581  34.814  1.00  0.00              
ATOM     49  N   THR    24      16.716  27.905  36.615  1.00  0.00              
ATOM     50  CA  THR    24      17.713  27.483  37.560  1.00  0.00              
ATOM     51  C   THR    24      18.263  26.107  37.223  1.00  0.00              
ATOM     52  O   THR    24      17.519  25.168  36.983  1.00  0.00              
ATOM     53  N   GLY    25      19.574  25.932  37.187  1.00  0.00              
ATOM     54  CA  GLY    25      20.038  24.599  36.852  1.00  0.00              
ATOM     55  C   GLY    25      20.383  23.686  38.011  1.00  0.00              
ATOM     56  O   GLY    25      19.710  22.715  38.333  1.00  0.00              
ATOM     57  N   GLU    26      21.447  24.045  38.634  1.00  0.00              
ATOM     58  CA  GLU    26      21.929  23.303  39.707  1.00  0.00              
ATOM     59  C   GLU    26      22.087  24.132  40.932  1.00  0.00              
ATOM     60  O   GLU    26      22.453  25.290  40.774  1.00  0.00              
ATOM     61  N   VAL    27      21.869  23.501  42.113  1.00  0.00              
ATOM     62  CA  VAL    27      22.078  24.125  43.393  1.00  0.00              
ATOM     63  C   VAL    27      23.029  23.279  44.257  1.00  0.00              
ATOM     64  O   VAL    27      22.706  22.159  44.584  1.00  0.00              
ATOM     65  N   LEU    32      26.377  27.664  45.918  1.00  0.00              
ATOM     66  CA  LEU    32      26.638  27.951  44.506  1.00  0.00              
ATOM     67  C   LEU    32      25.459  27.462  43.691  1.00  0.00              
ATOM     68  O   LEU    32      24.784  26.584  44.163  1.00  0.00              
ATOM     69  N   ILE    33      25.206  28.022  42.493  1.00  0.00              
ATOM     70  CA  ILE    33      24.100  27.619  41.612  1.00  0.00              
ATOM     71  C   ILE    33      24.433  27.983  40.181  1.00  0.00              
ATOM     72  O   ILE    33      25.266  28.831  39.906  1.00  0.00              
ATOM     73  N   GLU    34      23.734  27.373  39.264  1.00  0.00              
ATOM     74  CA  GLU    34      23.912  27.653  37.856  1.00  0.00              
ATOM     75  C   GLU    34      22.572  28.097  37.383  1.00  0.00              
ATOM     76  O   GLU    34      21.583  27.842  38.059  1.00  0.00              
ATOM     77  N   ALA    35      22.570  28.673  36.200  1.00  0.00              
ATOM     78  CA  ALA    35      21.378  29.145  35.599  1.00  0.00              
ATOM     79  C   ALA    35      21.548  29.375  34.118  1.00  0.00              
ATOM     80  O   ALA    35      22.535  29.959  33.690  1.00  0.00              
ATOM     81  N   GLU    36      20.587  28.903  33.330  1.00  0.00              
ATOM     82  CA  GLU    36      20.669  29.167  31.907  1.00  0.00              
ATOM     83  C   GLU    36      19.599  30.154  31.466  1.00  0.00              
ATOM     84  O   GLU    36      18.396  29.938  31.601  1.00  0.00              
ATOM     85  N   ASP    37      20.030  31.285  30.970  1.00  0.00              
ATOM     86  CA  ASP    37      19.104  32.305  30.524  1.00  0.00              
ATOM     87  C   ASP    37      18.313  31.825  29.303  1.00  0.00              
ATOM     88  O   ASP    37      18.709  30.907  28.549  1.00  0.00              
ATOM     89  N   ASN    45      24.709  30.794  29.810  1.00  0.00              
ATOM     90  CA  ASN    45      24.854  29.882  30.899  1.00  0.00              
ATOM     91  C   ASN    45      25.819  30.406  31.938  1.00  0.00              
ATOM     92  O   ASN    45      27.008  30.524  31.693  1.00  0.00              
ATOM     93  N   ILE    46      25.308  30.696  33.121  1.00  0.00              
ATOM     94  CA  ILE    46      26.173  31.198  34.150  1.00  0.00              
ATOM     95  C   ILE    46      26.244  30.405  35.454  1.00  0.00              
ATOM     96  O   ILE    46      25.355  29.641  35.721  1.00  0.00              
ATOM     97  N   THR    47      27.313  30.621  36.239  1.00  0.00              
ATOM     98  CA  THR    47      27.516  29.905  37.455  1.00  0.00              
ATOM     99  C   THR    47      27.873  30.884  38.513  1.00  0.00              
ATOM    100  O   THR    47      28.743  31.669  38.291  1.00  0.00              
ATOM    101  N   VAL    48      27.216  30.857  39.666  1.00  0.00              
ATOM    102  CA  VAL    48      27.529  31.813  40.703  1.00  0.00              
ATOM    103  C   VAL    48      28.037  31.077  41.912  1.00  0.00              
ATOM    104  O   VAL    48      27.358  30.216  42.355  1.00  0.00              
ATOM    105  N   THR    49      29.222  31.411  42.444  1.00  0.00              
ATOM    106  CA  THR    49      29.764  30.649  43.561  1.00  0.00              
ATOM    107  C   THR    49      30.105  31.485  44.721  1.00  0.00              
ATOM    108  O   THR    49      31.004  32.267  44.623  1.00  0.00              
ATOM    109  N   VAL    55      23.812  29.536  54.779  1.00  0.00              
ATOM    110  CA  VAL    55      23.046  29.546  53.549  1.00  0.00              
ATOM    111  C   VAL    55      21.646  28.862  53.695  1.00  0.00              
ATOM    112  O   VAL    55      21.490  27.749  54.194  1.00  0.00              
ATOM    113  N   ALA    56      20.619  29.536  53.202  1.00  0.00              
ATOM    114  CA  ALA    56      19.241  29.084  53.180  1.00  0.00              
ATOM    115  C   ALA    56      18.808  29.081  51.742  1.00  0.00              
ATOM    116  O   ALA    56      18.801  30.117  51.063  1.00  0.00              
ATOM    117  N   GLN    57      18.393  27.965  51.291  1.00  0.00              
ATOM    118  CA  GLN    57      17.967  27.885  49.927  1.00  0.00              
ATOM    119  C   GLN    57      16.512  28.135  49.658  1.00  0.00              
ATOM    120  O   GLN    57      15.646  27.353  50.006  1.00  0.00              
ATOM    121  N   GLN    60      11.955  28.143  37.276  1.00  0.00              
ATOM    122  CA  GLN    60      12.061  29.160  36.284  1.00  0.00              
ATOM    123  C   GLN    60      12.028  30.440  37.069  1.00  0.00              
ATOM    124  O   GLN    60      11.170  30.619  37.923  1.00  0.00              
ATOM    125  N   VAL    61      12.984  31.312  36.823  1.00  0.00              
ATOM    126  CA  VAL    61      13.028  32.539  37.582  1.00  0.00              
ATOM    127  C   VAL    61      13.215  33.724  36.683  1.00  0.00              
ATOM    128  O   VAL    61      13.454  33.570  35.471  1.00  0.00              
ATOM    129  N   SER    66      14.891  35.589  44.245  1.00  0.00              
ATOM    130  CA  SER    66      15.731  34.969  45.283  1.00  0.00              
ATOM    131  C   SER    66      16.045  33.522  45.007  1.00  0.00              
ATOM    132  O   SER    66      15.141  32.754  44.695  1.00  0.00              
ATOM    133  N   LYS    67      17.343  33.175  45.139  1.00  0.00              
ATOM    134  CA  LYS    67      17.800  31.827  44.975  1.00  0.00              
ATOM    135  C   LYS    67      18.306  31.304  46.325  1.00  0.00              
ATOM    136  O   LYS    67      17.970  30.200  46.760  1.00  0.00              
ATOM    137  N   ILE    68      19.138  32.112  46.980  1.00  0.00              
ATOM    138  CA  ILE    68      19.714  31.724  48.264  1.00  0.00              
ATOM    139  C   ILE    68      19.815  32.925  49.178  1.00  0.00              
ATOM    140  O   ILE    68      20.090  34.052  48.742  1.00  0.00              
ATOM    141  N   ARG    69      19.584  32.630  50.470  1.00  0.00              
ATOM    142  CA  ARG    69      19.677  33.617  51.491  1.00  0.00              
ATOM    143  C   ARG    69      20.881  33.219  52.299  1.00  0.00              
ATOM    144  O   ARG    69      21.099  32.033  52.518  1.00  0.00              
ATOM    145  N   PHE    70      21.706  34.176  52.687  1.00  0.00              
ATOM    146  CA  PHE    70      22.919  33.824  53.440  1.00  0.00              
ATOM    147  C   PHE    70      23.224  34.766  54.643  1.00  0.00              
ATOM    148  O   PHE    70      22.841  35.936  54.700  1.00  0.00              
END
