REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0059AL009_3 
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  3   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1sto 
ATOM      1  N   SER     2      30.043  14.736   1.474  1.00  0.00              
ATOM      2  CA  SER     2      30.708  15.992   1.679  1.00  0.00              
ATOM      3  C   SER     2      31.155  16.574   0.396  1.00  0.00              
ATOM      4  O   SER     2      31.500  15.872  -0.561  1.00  0.00              
ATOM      5  N   ILE     3      31.251  17.871   0.481  1.00  0.00              
ATOM      6  CA  ILE     3      31.620  18.704  -0.603  1.00  0.00              
ATOM      7  C   ILE     3      32.818  19.536  -0.237  1.00  0.00              
ATOM      8  O   ILE     3      32.701  20.560   0.439  1.00  0.00              
ATOM      9  N   GLY     4      33.949  19.119  -0.734  1.00  0.00              
ATOM     10  CA  GLY     4      35.171  19.834  -0.509  1.00  0.00              
ATOM     11  C   GLY     4      36.206  18.882   0.023  1.00  0.00              
ATOM     12  O   GLY     4      36.136  17.682  -0.235  1.00  0.00              
ATOM     13  N   GLY    15      40.829  14.757  10.334  1.00  0.00              
ATOM     14  CA  GLY    15      41.502  15.477  11.394  1.00  0.00              
ATOM     15  C   GLY    15      40.588  16.334  12.268  1.00  0.00              
ATOM     16  O   GLY    15      39.488  15.905  12.623  1.00  0.00              
ATOM     17  N   HIS    16      41.092  17.545  12.642  1.00  0.00              
ATOM     18  CA  HIS    16      40.445  18.463  13.605  1.00  0.00              
ATOM     19  C   HIS    16      39.537  19.488  12.960  1.00  0.00              
ATOM     20  O   HIS    16      39.983  20.594  12.581  1.00  0.00              
ATOM     21  N   ILE    17      38.251  19.150  12.885  1.00  0.00              
ATOM     22  CA  ILE    17      37.306  20.022  12.257  1.00  0.00              
ATOM     23  C   ILE    17      37.021  21.219  13.071  1.00  0.00              
ATOM     24  O   ILE    17      36.724  21.087  14.210  1.00  0.00              
ATOM     25  N   VAL    18      36.899  22.368  12.479  1.00  0.00              
ATOM     26  CA  VAL    18      36.345  23.502  13.099  1.00  0.00              
ATOM     27  C   VAL    18      35.056  23.812  12.427  1.00  0.00              
ATOM     28  O   VAL    18      34.950  24.050  11.210  1.00  0.00              
ATOM     29  N   THR    19      34.058  23.684  13.234  1.00  0.00              
ATOM     30  CA  THR    19      32.706  23.877  12.816  1.00  0.00              
ATOM     31  C   THR    19      32.346  25.362  12.925  1.00  0.00              
ATOM     32  O   THR    19      32.875  26.082  13.749  1.00  0.00              
ATOM     33  N   CYS    20      31.492  25.829  12.052  1.00  0.00              
ATOM     34  CA  CYS    20      31.214  27.229  11.901  1.00  0.00              
ATOM     35  C   CYS    20      29.753  27.409  11.560  1.00  0.00              
ATOM     36  O   CYS    20      29.238  26.683  10.723  1.00  0.00              
ATOM     37  N   LEU    32      24.088  20.642  15.036  1.00  0.00              
ATOM     38  CA  LEU    32      25.415  20.289  15.549  1.00  0.00              
ATOM     39  C   LEU    32      25.414  18.781  15.814  1.00  0.00              
ATOM     40  O   LEU    32      26.324  18.043  15.433  1.00  0.00              
ATOM     41  N   ILE    33      24.333  18.320  16.449  1.00  0.00              
ATOM     42  CA  ILE    33      24.170  16.910  16.738  1.00  0.00              
ATOM     43  C   ILE    33      23.885  16.090  15.480  1.00  0.00              
ATOM     44  O   ILE    33      23.716  14.880  15.535  1.00  0.00              
ATOM     45  N   GLU    34      23.812  16.772  14.348  1.00  0.00              
ATOM     46  CA  GLU    34      23.624  16.135  13.038  1.00  0.00              
ATOM     47  C   GLU    34      24.947  16.289  12.354  1.00  0.00              
ATOM     48  O   GLU    34      25.643  15.351  11.925  1.00  0.00              
ATOM     49  N   ALA    35      25.309  17.530  12.418  1.00  0.00              
ATOM     50  CA  ALA    35      26.507  17.988  11.891  1.00  0.00              
ATOM     51  C   ALA    35      27.625  17.220  12.503  1.00  0.00              
ATOM     52  O   ALA    35      28.503  16.750  11.848  1.00  0.00              
ATOM     53  N   GLU    36      27.549  17.050  13.778  1.00  0.00              
ATOM     54  CA  GLU    36      28.623  16.442  14.487  1.00  0.00              
ATOM     55  C   GLU    36      28.577  14.934  14.432  1.00  0.00              
ATOM     56  O   GLU    36      29.570  14.256  14.690  1.00  0.00              
ATOM     57  N   ASP    37      27.450  14.436  13.884  1.00  0.00              
ATOM     58  CA  ASP    37      27.283  13.027  13.565  1.00  0.00              
ATOM     59  C   ASP    37      28.228  12.700  12.429  1.00  0.00              
ATOM     60  O   ASP    37      29.126  11.894  12.586  1.00  0.00              
ATOM     61  N   ASN    38      28.069  13.419  11.304  1.00  0.00              
ATOM     62  CA  ASN    38      28.992  13.381  10.172  1.00  0.00              
ATOM     63  C   ASN    38      30.443  13.370  10.611  1.00  0.00              
ATOM     64  O   ASN    38      31.213  12.506  10.213  1.00  0.00              
ATOM     65  N   MET    39      30.875  14.450  11.265  1.00  0.00              
ATOM     66  CA  MET    39      32.279  14.563  11.610  1.00  0.00              
ATOM     67  C   MET    39      32.787  13.350  12.350  1.00  0.00              
ATOM     68  O   MET    39      33.852  12.784  12.040  1.00  0.00              
ATOM     69  N   ASN    40      32.043  12.989  13.374  1.00  0.00              
ATOM     70  CA  ASN    40      32.383  11.837  14.120  1.00  0.00              
ATOM     71  C   ASN    40      32.091  10.542  13.369  1.00  0.00              
ATOM     72  O   ASN    40      32.529   9.473  13.789  1.00  0.00              
ATOM     73  N   CYS    41      37.022  11.952  12.051  1.00  0.00              
ATOM     74  CA  CYS    41      37.647  13.254  12.218  1.00  0.00              
ATOM     75  C   CYS    41      37.287  13.680  13.645  1.00  0.00              
ATOM     76  O   CYS    41      36.202  13.341  14.071  1.00  0.00              
ATOM     77  N   GLN    42      38.156  14.353  14.421  1.00  0.00              
ATOM     78  CA  GLN    42      37.619  14.849  15.695  1.00  0.00              
ATOM     79  C   GLN    42      36.945  16.197  15.476  1.00  0.00              
ATOM     80  O   GLN    42      37.044  16.781  14.390  1.00  0.00              
ATOM     81  N   MET    43      36.368  16.725  16.564  1.00  0.00              
ATOM     82  CA  MET    43      35.808  18.071  16.622  1.00  0.00              
ATOM     83  C   MET    43      36.675  18.936  17.482  1.00  0.00              
ATOM     84  O   MET    43      37.047  18.535  18.564  1.00  0.00              
ATOM     85  N   SER    44      37.058  20.090  16.956  1.00  0.00              
ATOM     86  CA  SER    44      37.868  21.033  17.670  1.00  0.00              
ATOM     87  C   SER    44      36.988  22.080  18.250  1.00  0.00              
ATOM     88  O   SER    44      37.289  22.569  19.319  1.00  0.00              
ATOM     89  N   ASN    45      35.896  22.449  17.580  1.00  0.00              
ATOM     90  CA  ASN    45      35.078  23.492  18.182  1.00  0.00              
ATOM     91  C   ASN    45      33.966  23.984  17.318  1.00  0.00              
ATOM     92  O   ASN    45      33.722  23.456  16.263  1.00  0.00              
ATOM     93  N   ILE    46      33.314  25.017  17.798  1.00  0.00              
ATOM     94  CA  ILE    46      32.218  25.714  17.119  1.00  0.00              
ATOM     95  C   ILE    46      32.370  27.238  17.254  1.00  0.00              
ATOM     96  O   ILE    46      32.489  27.844  18.317  1.00  0.00              
ATOM     97  N   THR    47      32.440  27.846  16.139  1.00  0.00              
ATOM     98  CA  THR    47      32.657  29.239  16.067  1.00  0.00              
ATOM     99  C   THR    47      31.318  29.827  15.708  1.00  0.00              
ATOM    100  O   THR    47      30.679  29.279  14.864  1.00  0.00              
ATOM    101  N   VAL    48      30.812  30.817  16.424  1.00  0.00              
ATOM    102  CA  VAL    48      29.512  31.365  16.124  1.00  0.00              
ATOM    103  C   VAL    48      29.568  32.869  16.177  1.00  0.00              
ATOM    104  O   VAL    48      30.644  33.444  16.395  1.00  0.00              
ATOM    105  N   THR    49      28.417  33.515  15.966  1.00  0.00              
ATOM    106  CA  THR    49      28.335  34.976  16.004  1.00  0.00              
ATOM    107  C   THR    49      27.963  35.555  17.377  1.00  0.00              
ATOM    108  O   THR    49      28.568  36.504  17.881  1.00  0.00              
ATOM    109  N   TYR    50      26.973  34.971  17.965  1.00  0.00              
ATOM    110  CA  TYR    50      26.334  35.495  19.109  1.00  0.00              
ATOM    111  C   TYR    50      25.895  34.413  20.010  1.00  0.00              
ATOM    112  O   TYR    50      24.971  33.639  19.636  1.00  0.00              
ATOM    113  N   ARG    51      26.531  34.462  21.211  1.00  0.00              
ATOM    114  CA  ARG    51      26.180  33.804  22.452  1.00  0.00              
ATOM    115  C   ARG    51      25.165  34.648  23.286  1.00  0.00              
ATOM    116  O   ARG    51      25.523  35.690  23.905  1.00  0.00              
ATOM    117  N   ARG    54      22.672  26.680  26.079  1.00  0.00              
ATOM    118  CA  ARG    54      22.848  25.802  24.924  1.00  0.00              
ATOM    119  C   ARG    54      24.277  25.687  24.510  1.00  0.00              
ATOM    120  O   ARG    54      24.714  24.663  23.998  1.00  0.00              
ATOM    121  N   VAL    55      24.946  26.793  24.575  1.00  0.00              
ATOM    122  CA  VAL    55      26.292  26.710  24.245  1.00  0.00              
ATOM    123  C   VAL    55      26.916  25.755  25.258  1.00  0.00              
ATOM    124  O   VAL    55      27.417  24.687  24.904  1.00  0.00              
ATOM    125  N   ALA    56      26.673  26.049  26.532  1.00  0.00              
ATOM    126  CA  ALA    56      27.169  25.273  27.663  1.00  0.00              
ATOM    127  C   ALA    56      26.859  23.801  27.523  1.00  0.00              
ATOM    128  O   ALA    56      27.692  22.932  27.809  1.00  0.00              
ATOM    129  N   GLN    57      25.657  23.528  27.077  1.00  0.00              
ATOM    130  CA  GLN    57      25.261  22.167  26.834  1.00  0.00              
ATOM    131  C   GLN    57      26.046  21.584  25.703  1.00  0.00              
ATOM    132  O   GLN    57      26.413  20.418  25.760  1.00  0.00              
ATOM    133  N   LEU    58      26.258  22.389  24.637  1.00  0.00              
ATOM    134  CA  LEU    58      27.097  21.959  23.529  1.00  0.00              
ATOM    135  C   LEU    58      28.489  21.597  24.051  1.00  0.00              
ATOM    136  O   LEU    58      28.869  20.452  23.923  1.00  0.00              
ATOM    137  N   GLU    59      29.172  22.513  24.793  1.00  0.00              
ATOM    138  CA  GLU    59      30.473  22.216  25.402  1.00  0.00              
ATOM    139  C   GLU    59      30.387  20.953  26.275  1.00  0.00              
ATOM    140  O   GLU    59      31.294  20.105  26.340  1.00  0.00              
ATOM    141  N   GLN    60      29.280  20.880  27.003  1.00  0.00              
ATOM    142  CA  GLN    60      28.973  19.832  27.969  1.00  0.00              
ATOM    143  C   GLN    60      28.635  18.478  27.337  1.00  0.00              
ATOM    144  O   GLN    60      28.463  17.521  28.058  1.00  0.00              
ATOM    145  N   VAL    61      28.503  18.392  25.999  1.00  0.00              
ATOM    146  CA  VAL    61      28.096  17.137  25.329  1.00  0.00              
ATOM    147  C   VAL    61      29.029  16.607  24.218  1.00  0.00              
ATOM    148  O   VAL    61      29.051  15.395  23.958  1.00  0.00              
ATOM    149  N   TYR    62      29.766  17.499  23.547  1.00  0.00              
ATOM    150  CA  TYR    62      30.666  17.112  22.476  1.00  0.00              
ATOM    151  C   TYR    62      32.149  17.326  22.818  1.00  0.00              
ATOM    152  O   TYR    62      33.051  17.226  21.934  1.00  0.00              
ATOM    153  N   LYS    67      34.888  22.972  22.297  1.00  0.00              
ATOM    154  CA  LYS    67      34.841  24.312  22.799  1.00  0.00              
ATOM    155  C   LYS    67      34.216  25.263  21.778  1.00  0.00              
ATOM    156  O   LYS    67      34.548  25.212  20.614  1.00  0.00              
ATOM    157  N   ILE    68      33.170  25.963  22.200  1.00  0.00              
ATOM    158  CA  ILE    68      32.539  26.918  21.362  1.00  0.00              
ATOM    159  C   ILE    68      33.193  28.234  21.560  1.00  0.00              
ATOM    160  O   ILE    68      33.108  28.747  22.641  1.00  0.00              
ATOM    161  N   ARG    69      33.699  28.803  20.478  1.00  0.00              
ATOM    162  CA  ARG    69      34.170  30.155  20.404  1.00  0.00              
ATOM    163  C   ARG    69      33.026  31.007  19.825  1.00  0.00              
ATOM    164  O   ARG    69      32.008  30.446  19.391  1.00  0.00              
ATOM    165  N   PHE    70      33.183  32.350  19.784  1.00  0.00              
ATOM    166  CA  PHE    70      32.112  33.199  19.302  1.00  0.00              
ATOM    167  C   PHE    70      32.436  34.697  19.341  1.00  0.00              
ATOM    168  O   PHE    70      33.227  35.180  20.119  1.00  0.00              
ATOM    169  N   LEU    71      31.829  35.452  18.480  1.00  0.00              
ATOM    170  CA  LEU    71      32.241  36.814  18.350  1.00  0.00              
ATOM    171  C   LEU    71      31.732  37.773  19.390  1.00  0.00              
ATOM    172  O   LEU    71      32.505  38.499  19.966  1.00  0.00              
ATOM    173  N   ILE    72      30.426  37.970  19.442  1.00  0.00              
ATOM    174  CA  ILE    72      29.938  38.740  20.505  1.00  0.00              
ATOM    175  C   ILE    72      29.276  37.812  21.483  1.00  0.00              
ATOM    176  O   ILE    72      29.132  36.625  21.210  1.00  0.00              
ATOM    177  N   LEU    73      29.040  38.345  22.673  1.00  0.00              
ATOM    178  CA  LEU    73      28.228  37.725  23.702  1.00  0.00              
ATOM    179  C   LEU    73      27.310  38.828  24.215  1.00  0.00              
ATOM    180  O   LEU    73      27.504  39.996  23.886  1.00  0.00              
END
