REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0059AL009_5 
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  5  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1mjc 
ATOM      1  N   ILE     3      18.507  22.381  33.304  1.00  0.00              
ATOM      2  CA  ILE     3      18.958  21.022  32.935  1.00  0.00              
ATOM      3  C   ILE     3      20.341  20.854  33.573  1.00  0.00              
ATOM      4  O   ILE     3      21.041  21.819  33.892  1.00  0.00              
ATOM      5  N   GLY     4      20.750  19.643  33.798  1.00  0.00              
ATOM      6  CA  GLY     4      22.092  19.382  34.362  1.00  0.00              
ATOM      7  C   GLY     4      22.806  18.608  33.249  1.00  0.00              
ATOM      8  O   GLY     4      22.191  18.029  32.331  1.00  0.00              
ATOM      9  N   VAL     5      24.111  18.605  33.293  1.00  0.00              
ATOM     10  CA  VAL     5      24.906  17.886  32.277  1.00  0.00              
ATOM     11  C   VAL     5      26.382  17.874  32.687  1.00  0.00              
ATOM     12  O   VAL     5      26.694  18.286  33.791  1.00  0.00              
ATOM     13  N   PRO     6      27.223  17.419  31.803  1.00  0.00              
ATOM     14  CA  PRO     6      28.671  17.339  32.005  1.00  0.00              
ATOM     15  C   PRO     6      29.383  18.068  30.910  1.00  0.00              
ATOM     16  O   PRO     6      28.882  17.912  29.796  1.00  0.00              
ATOM     17  N   ILE     7      30.466  18.746  31.125  1.00  0.00              
ATOM     18  CA  ILE     7      31.222  19.420  30.035  1.00  0.00              
ATOM     19  C   ILE     7      31.909  18.302  29.227  1.00  0.00              
ATOM     20  O   ILE     7      32.708  17.494  29.758  1.00  0.00              
ATOM     21  N   LYS     8      31.610  18.237  27.940  1.00  0.00              
ATOM     22  CA  LYS     8      32.125  17.280  26.971  1.00  0.00              
ATOM     23  C   LYS     8      33.528  17.775  26.696  1.00  0.00              
ATOM     24  O   LYS     8      34.481  17.013  26.862  1.00  0.00              
ATOM     25  N   VAL     9      33.652  19.030  26.332  1.00  0.00              
ATOM     26  CA  VAL     9      34.998  19.635  26.091  1.00  0.00              
ATOM     27  C   VAL     9      34.851  21.138  26.196  1.00  0.00              
ATOM     28  O   VAL     9      33.699  21.618  26.122  1.00  0.00              
ATOM     29  N   LEU    10      35.953  21.862  26.374  1.00  0.00              
ATOM     30  CA  LEU    10      35.817  23.332  26.442  1.00  0.00              
ATOM     31  C   LEU    10      37.114  23.913  25.858  1.00  0.00              
ATOM     32  O   LEU    10      38.102  23.524  26.494  1.00  0.00              
ATOM     33  N   HIS    11      37.082  24.714  24.805  1.00  0.00              
ATOM     34  CA  HIS    11      38.312  25.273  24.243  1.00  0.00              
ATOM     35  C   HIS    11      38.498  26.657  24.848  1.00  0.00              
ATOM     36  O   HIS    11      37.877  27.568  24.307  1.00  0.00              
ATOM     37  N   GLU    14      34.621  28.489  23.907  1.00  0.00              
ATOM     38  CA  GLU    14      33.334  27.763  23.692  1.00  0.00              
ATOM     39  C   GLU    14      33.592  26.253  23.840  1.00  0.00              
ATOM     40  O   GLU    14      34.770  25.850  23.787  1.00  0.00              
ATOM     41  N   GLY    15      32.473  25.535  23.917  1.00  0.00              
ATOM     42  CA  GLY    15      32.600  24.059  24.031  1.00  0.00              
ATOM     43  C   GLY    15      31.184  23.480  23.985  1.00  0.00              
ATOM     44  O   GLY    15      30.287  24.180  23.527  1.00  0.00              
ATOM     45  N   HIS    16      31.087  22.251  24.462  1.00  0.00              
ATOM     46  CA  HIS    16      29.816  21.523  24.494  1.00  0.00              
ATOM     47  C   HIS    16      29.617  20.873  25.845  1.00  0.00              
ATOM     48  O   HIS    16      30.577  20.528  26.519  1.00  0.00              
ATOM     49  N   ILE    17      28.363  20.712  26.148  1.00  0.00              
ATOM     50  CA  ILE    17      27.756  20.102  27.301  1.00  0.00              
ATOM     51  C   ILE    17      26.904  18.920  26.791  1.00  0.00              
ATOM     52  O   ILE    17      26.203  19.085  25.813  1.00  0.00              
ATOM     53  N   VAL    18      27.000  17.821  27.476  1.00  0.00              
ATOM     54  CA  VAL    18      26.232  16.583  27.242  1.00  0.00              
ATOM     55  C   VAL    18      25.137  16.621  28.340  1.00  0.00              
ATOM     56  O   VAL    18      25.425  16.464  29.533  1.00  0.00              
ATOM     57  N   THR    19      23.901  16.865  27.929  1.00  0.00              
ATOM     58  CA  THR    19      22.773  16.965  28.854  1.00  0.00              
ATOM     59  C   THR    19      22.483  15.639  29.489  1.00  0.00              
ATOM     60  O   THR    19      22.665  14.648  28.804  1.00  0.00              
ATOM     61  N   VAL    27      24.915  20.420  23.776  1.00  0.00              
ATOM     62  CA  VAL    27      24.567  21.836  23.795  1.00  0.00              
ATOM     63  C   VAL    27      25.804  22.711  23.757  1.00  0.00              
ATOM     64  O   VAL    27      26.664  22.525  24.624  1.00  0.00              
ATOM     65  N   TYR    28      25.809  23.632  22.844  1.00  0.00              
ATOM     66  CA  TYR    28      26.907  24.614  22.694  1.00  0.00              
ATOM     67  C   TYR    28      26.990  25.506  23.922  1.00  0.00              
ATOM     68  O   TYR    28      25.909  25.973  24.330  1.00  0.00              
ATOM     69  N   ARG    29      28.165  25.787  24.475  1.00  0.00              
ATOM     70  CA  ARG    29      28.225  26.715  25.607  1.00  0.00              
ATOM     71  C   ARG    29      29.269  27.777  25.143  1.00  0.00              
ATOM     72  O   ARG    29      30.362  27.429  24.654  1.00  0.00              
ATOM     73  N   GLY    30      28.947  29.042  25.317  1.00  0.00              
ATOM     74  CA  GLY    30      29.825  30.169  24.991  1.00  0.00              
ATOM     75  C   GLY    30      30.420  30.672  26.309  1.00  0.00              
ATOM     76  O   GLY    30      29.661  30.586  27.287  1.00  0.00              
ATOM     77  N   ASN    45      30.390  18.859  36.270  1.00  0.00              
ATOM     78  CA  ASN    45      28.906  18.778  36.294  1.00  0.00              
ATOM     79  C   ASN    45      28.455  20.220  36.209  1.00  0.00              
ATOM     80  O   ASN    45      29.053  21.084  36.868  1.00  0.00              
ATOM     81  N   ILE    46      27.489  20.603  35.428  1.00  0.00              
ATOM     82  CA  ILE    46      27.016  21.971  35.287  1.00  0.00              
ATOM     83  C   ILE    46      25.493  21.924  35.225  1.00  0.00              
ATOM     84  O   ILE    46      24.883  20.858  35.015  1.00  0.00              
ATOM     85  N   THR    47      24.924  23.086  35.402  1.00  0.00              
ATOM     86  CA  THR    47      23.460  23.309  35.352  1.00  0.00              
ATOM     87  C   THR    47      23.412  24.550  34.468  1.00  0.00              
ATOM     88  O   THR    47      24.244  25.463  34.459  1.00  0.00              
ATOM     89  N   VAL    48      22.378  24.539  33.658  1.00  0.00              
ATOM     90  CA  VAL    48      22.139  25.556  32.635  1.00  0.00              
ATOM     91  C   VAL    48      20.726  25.567  32.137  1.00  0.00              
ATOM     92  O   VAL    48      20.037  24.592  32.462  1.00  0.00              
ATOM     93  N   THR    49      20.358  26.546  31.376  1.00  0.00              
ATOM     94  CA  THR    49      19.003  26.574  30.796  1.00  0.00              
ATOM     95  C   THR    49      19.253  26.357  29.321  1.00  0.00              
ATOM     96  O   THR    49      20.368  26.690  28.851  1.00  0.00              
ATOM     97  N   TYR    50      18.313  25.827  28.589  1.00  0.00              
ATOM     98  CA  TYR    50      18.475  25.605  27.134  1.00  0.00              
ATOM     99  C   TYR    50      17.816  26.861  26.528  1.00  0.00              
ATOM    100  O   TYR    50      16.681  27.263  26.829  1.00  0.00              
ATOM    101  N   ARG    51      18.621  27.420  25.649  1.00  0.00              
ATOM    102  CA  ARG    51      18.208  28.643  24.993  1.00  0.00              
ATOM    103  C   ARG    51      18.323  28.537  23.496  1.00  0.00              
ATOM    104  O   ARG    51      18.881  27.626  22.893  1.00  0.00              
ATOM    105  N   GLN    57      21.655  26.065  22.795  1.00  0.00              
ATOM    106  CA  GLN    57      22.688  26.755  23.544  1.00  0.00              
ATOM    107  C   GLN    57      22.384  26.772  25.034  1.00  0.00              
ATOM    108  O   GLN    57      21.209  26.778  25.445  1.00  0.00              
ATOM    109  N   LEU    58      23.430  26.784  25.819  1.00  0.00              
ATOM    110  CA  LEU    58      23.318  26.799  27.272  1.00  0.00              
ATOM    111  C   LEU    58      23.326  28.246  27.725  1.00  0.00              
ATOM    112  O   LEU    58      24.141  29.008  27.185  1.00  0.00              
ATOM    113  N   GLU    59      22.468  28.571  28.657  1.00  0.00              
ATOM    114  CA  GLU    59      22.383  29.927  29.234  1.00  0.00              
ATOM    115  C   GLU    59      22.486  29.658  30.741  1.00  0.00              
ATOM    116  O   GLU    59      22.227  28.533  31.205  1.00  0.00              
ATOM    117  N   GLN    60      22.867  30.669  31.511  1.00  0.00              
ATOM    118  CA  GLN    60      22.992  30.645  32.981  1.00  0.00              
ATOM    119  C   GLN    60      23.698  29.424  33.504  1.00  0.00              
ATOM    120  O   GLN    60      23.194  28.710  34.396  1.00  0.00              
ATOM    121  N   VAL    61      24.872  29.177  32.973  1.00  0.00              
ATOM    122  CA  VAL    61      25.709  28.020  33.327  1.00  0.00              
ATOM    123  C   VAL    61      26.342  28.224  34.690  1.00  0.00              
ATOM    124  O   VAL    61      27.095  29.174  34.927  1.00  0.00              
ATOM    125  N   TYR    62      26.014  27.250  35.495  1.00  0.00              
ATOM    126  CA  TYR    62      26.437  27.134  36.881  1.00  0.00              
ATOM    127  C   TYR    62      27.213  25.889  37.167  1.00  0.00              
ATOM    128  O   TYR    62      26.857  24.918  36.525  1.00  0.00              
ATOM    129  N   ILE    63      28.152  25.873  38.066  1.00  0.00              
ATOM    130  CA  ILE    63      28.896  24.653  38.406  1.00  0.00              
ATOM    131  C   ILE    63      28.086  23.914  39.464  1.00  0.00              
ATOM    132  O   ILE    63      27.388  24.541  40.255  1.00  0.00              
END
