REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0072AL009_1 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0072  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0072, CDS domain 1  
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  1 UNREFINED  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 2mcm 
ATOM      1  N   ASP     6      30.098  15.570   1.812  1.00  0.00              
ATOM      2  CA  ASP     6      29.367  14.443   1.133  1.00  0.00              
ATOM      3  C   ASP     6      28.419  13.747   2.104  1.00  0.00              
ATOM      4  O   ASP     6      28.923  12.833   2.813  1.00  0.00              
ATOM      5  N   PRO     7      27.138  14.063   2.104  1.00  0.00              
ATOM      6  CA  PRO     7      26.234  13.470   3.094  1.00  0.00              
ATOM      7  C   PRO     7      26.083  11.984   3.087  1.00  0.00              
ATOM      8  O   PRO     7      25.869  11.337   2.052  1.00  0.00              
ATOM      9  N   ASP     8      26.108  11.426   4.313  1.00  0.00              
ATOM     10  CA  ASP     8      25.885   9.976   4.471  1.00  0.00              
ATOM     11  C   ASP     8      25.082   9.873   5.829  1.00  0.00              
ATOM     12  O   ASP     8      25.348  10.722   6.684  1.00  0.00              
ATOM     13  N   PHE     9      24.240   8.881   5.855  1.00  0.00              
ATOM     14  CA  PHE     9      23.454   8.754   7.130  1.00  0.00              
ATOM     15  C   PHE     9      23.366   7.254   7.460  1.00  0.00              
ATOM     16  O   PHE     9      23.331   6.397   6.553  1.00  0.00              
ATOM     17  N   ALA    11      15.529  -1.845  11.166  1.00  0.00              
ATOM     18  CA  ALA    11      14.576  -2.896  10.769  1.00  0.00              
ATOM     19  C   ALA    11      13.914  -3.550  12.006  1.00  0.00              
ATOM     20  O   ALA    11      14.560  -3.472  13.057  1.00  0.00              
ATOM     21  N   ARG    12      12.766  -4.130  11.774  1.00  0.00              
ATOM     22  CA  ARG    12      11.987  -4.794  12.839  1.00  0.00              
ATOM     23  C   ARG    12      11.612  -3.749  13.904  1.00  0.00              
ATOM     24  O   ARG    12      11.581  -4.116  15.116  1.00  0.00              
ATOM     25  N   LEU    13      11.399  -2.509  13.511  1.00  0.00              
ATOM     26  CA  LEU    13      11.107  -1.478  14.550  1.00  0.00              
ATOM     27  C   LEU    13       9.689  -1.645  15.037  1.00  0.00              
ATOM     28  O   LEU    13       8.760  -2.154  14.456  1.00  0.00              
ATOM     29  N   GLN    23      12.525   4.752  19.583  1.00  0.00              
ATOM     30  CA  GLN    23      13.481   5.832  19.354  1.00  0.00              
ATOM     31  C   GLN    23      14.620   5.260  18.522  1.00  0.00              
ATOM     32  O   GLN    23      15.173   4.233  18.945  1.00  0.00              
ATOM     33  N   LEU    24      14.978   5.928  17.415  1.00  0.00              
ATOM     34  CA  LEU    24      16.170   5.402  16.654  1.00  0.00              
ATOM     35  C   LEU    24      17.231   6.497  16.687  1.00  0.00              
ATOM     36  O   LEU    24      16.879   7.666  17.051  1.00  0.00              
ATOM     37  N   GLU    25      18.468   6.205  16.365  1.00  0.00              
ATOM     38  CA  GLU    25      19.486   7.247  16.357  1.00  0.00              
ATOM     39  C   GLU    25      19.855   7.520  14.857  1.00  0.00              
ATOM     40  O   GLU    25      20.125   6.490  14.208  1.00  0.00              
ATOM     41  N   VAL    26      19.803   8.739  14.501  1.00  0.00              
ATOM     42  CA  VAL    26      20.194   9.112  13.087  1.00  0.00              
ATOM     43  C   VAL    26      21.587   9.688  13.180  1.00  0.00              
ATOM     44  O   VAL    26      21.764  10.715  13.871  1.00  0.00              
ATOM     45  N   TYR    27      22.588   9.130  12.558  1.00  0.00              
ATOM     46  CA  TYR    27      23.974   9.606  12.562  1.00  0.00              
ATOM     47  C   TYR    27      24.350   9.994  11.106  1.00  0.00              
ATOM     48  O   TYR    27      24.230   9.123  10.229  1.00  0.00              
ATOM     49  N   LEU    28      24.734  11.248  11.027  1.00  0.00              
ATOM     50  CA  LEU    28      25.099  11.714   9.640  1.00  0.00              
ATOM     51  C   LEU    28      26.464  12.308   9.677  1.00  0.00              
ATOM     52  O   LEU    28      26.968  12.848  10.671  1.00  0.00              
ATOM     53  N   LYS    29      27.143  12.197   8.514  1.00  0.00              
ATOM     54  CA  LYS    29      28.483  12.741   8.361  1.00  0.00              
ATOM     55  C   LYS    29      28.600  13.406   6.958  1.00  0.00              
ATOM     56  O   LYS    29      27.704  13.221   6.163  1.00  0.00              
ATOM     57  N   GLY    31      19.778  21.161   9.471  1.00  0.00              
ATOM     58  CA  GLY    31      19.158  20.041   8.784  1.00  0.00              
ATOM     59  C   GLY    31      17.871  19.636   9.486  1.00  0.00              
ATOM     60  O   GLY    31      17.836  19.625  10.765  1.00  0.00              
ATOM     61  N   TRP    32      16.823  19.369   8.792  1.00  0.00              
ATOM     62  CA  TRP    32      15.531  18.911   9.287  1.00  0.00              
ATOM     63  C   TRP    32      15.573  17.400   9.317  1.00  0.00              
ATOM     64  O   TRP    32      15.731  16.750   8.274  1.00  0.00              
ATOM     65  N   HIS    33      15.466  16.793  10.484  1.00  0.00              
ATOM     66  CA  HIS    33      15.497  15.328  10.712  1.00  0.00              
ATOM     67  C   HIS    33      14.123  14.795  10.765  1.00  0.00              
ATOM     68  O   HIS    33      13.217  15.417  11.493  1.00  0.00              
ATOM     69  N   MET    34      13.694  13.772  10.041  1.00  0.00              
ATOM     70  CA  MET    34      12.286  13.342  10.146  1.00  0.00              
ATOM     71  C   MET    34      12.038  11.988   9.512  1.00  0.00              
ATOM     72  O   MET    34      12.933  11.408   8.856  1.00  0.00              
ATOM     73  N   VAL    35      10.845  11.490   9.722  1.00  0.00              
ATOM     74  CA  VAL    35      10.374  10.214   9.137  1.00  0.00              
ATOM     75  C   VAL    35       9.434  10.623   8.019  1.00  0.00              
ATOM     76  O   VAL    35       8.510  11.433   8.139  1.00  0.00              
ATOM     77  N   CYS    36       9.694  10.083   6.804  1.00  0.00              
ATOM     78  CA  CYS    36       8.934  10.477   5.608  1.00  0.00              
ATOM     79  C   CYS    36       8.611   9.297   4.685  1.00  0.00              
ATOM     80  O   CYS    36       9.144   8.213   4.906  1.00  0.00              
ATOM     81  N   SER    37       7.829   9.574   3.665  1.00  0.00              
ATOM     82  CA  SER    37       7.473   8.544   2.678  1.00  0.00              
ATOM     83  C   SER    37       7.055   9.333   1.440  1.00  0.00              
ATOM     84  O   SER    37       6.775  10.491   1.508  1.00  0.00              
ATOM     85  N   GLN    38       7.034   8.590   0.315  1.00  0.00              
ATOM     86  CA  GLN    38       6.550   9.226  -0.945  1.00  0.00              
ATOM     87  C   GLN    38       5.034   8.999  -0.926  1.00  0.00              
ATOM     88  O   GLN    38       4.539   7.840  -0.941  1.00  0.00              
ATOM     89  N   SER    39       4.317  10.125  -0.851  1.00  0.00              
ATOM     90  CA  SER    39       2.841   9.980  -0.773  1.00  0.00              
ATOM     91  C   SER    39       2.274   9.933  -2.183  1.00  0.00              
ATOM     92  O   SER    39       1.303   9.226  -2.449  1.00  0.00              
ATOM     93  N   SER    44       6.149  13.782  -4.629  1.00  0.00              
ATOM     94  CA  SER    44       5.736  14.461  -3.383  1.00  0.00              
ATOM     95  C   SER    44       6.037  13.573  -2.138  1.00  0.00              
ATOM     96  O   SER    44       5.482  12.507  -1.969  1.00  0.00              
ATOM     97  N   LYS    45       6.899  14.145  -1.354  1.00  0.00              
ATOM     98  CA  LYS    45       7.328  13.519  -0.071  1.00  0.00              
ATOM     99  C   LYS    45       6.494  14.152   1.065  1.00  0.00              
ATOM    100  O   LYS    45       6.283  15.360   1.088  1.00  0.00              
ATOM    101  N   GLN    46       6.006  13.242   1.932  1.00  0.00              
ATOM    102  CA  GLN    46       5.245  13.768   3.109  1.00  0.00              
ATOM    103  C   GLN    46       5.991  13.296   4.362  1.00  0.00              
ATOM    104  O   GLN    46       6.500  12.155   4.355  1.00  0.00              
ATOM    105  N   TRP    47       6.065  14.035   5.450  1.00  0.00              
ATOM    106  CA  TRP    47       6.802  13.626   6.654  1.00  0.00              
ATOM    107  C   TRP    47       5.920  13.871   7.922  1.00  0.00              
ATOM    108  O   TRP    47       4.953  14.628   7.824  1.00  0.00              
ATOM    109  N   GLU    48       6.335  13.310   9.010  1.00  0.00              
ATOM    110  CA  GLU    48       5.635  13.466  10.334  1.00  0.00              
ATOM    111  C   GLU    48       6.186  14.753  10.941  1.00  0.00              
ATOM    112  O   GLU    48       7.295  14.788  11.421  1.00  0.00              
ATOM    113  N   SER    51      12.621  17.244  13.901  1.00  0.00              
ATOM    114  CA  SER    51      13.379  18.168  14.718  1.00  0.00              
ATOM    115  C   SER    51      14.448  18.847  13.889  1.00  0.00              
ATOM    116  O   SER    51      14.802  18.236  12.828  1.00  0.00              
ATOM    117  N   GLN    52      15.006  19.931  14.283  1.00  0.00              
ATOM    118  CA  GLN    52      16.088  20.631  13.529  1.00  0.00              
ATOM    119  C   GLN    52      17.362  20.524  14.276  1.00  0.00              
ATOM    120  O   GLN    52      17.376  20.816  15.528  1.00  0.00              
ATOM    121  N   ALA    53      18.502  20.205  13.653  1.00  0.00              
ATOM    122  CA  ALA    53      19.779  20.155  14.279  1.00  0.00              
ATOM    123  C   ALA    53      20.817  20.866  13.398  1.00  0.00              
ATOM    124  O   ALA    53      20.659  20.681  12.160  1.00  0.00              
ATOM    125  N   SER    54      21.664  21.647  13.923  1.00  0.00              
ATOM    126  CA  SER    54      22.745  22.319  13.135  1.00  0.00              
ATOM    127  C   SER    54      23.934  21.452  13.143  1.00  0.00              
ATOM    128  O   SER    54      24.477  20.898  14.137  1.00  0.00              
ATOM    129  N   VAL    56      26.054  15.232  12.603  1.00  0.00              
ATOM    130  CA  VAL    56      24.842  15.357  13.394  1.00  0.00              
ATOM    131  C   VAL    56      24.559  13.949  13.953  1.00  0.00              
ATOM    132  O   VAL    56      24.649  12.937  13.225  1.00  0.00              
ATOM    133  N   CYS    57      24.197  13.928  15.255  1.00  0.00              
ATOM    134  CA  CYS    57      23.762  12.620  15.836  1.00  0.00              
ATOM    135  C   CYS    57      22.444  13.018  16.545  1.00  0.00              
ATOM    136  O   CYS    57      22.585  13.907  17.430  1.00  0.00              
ATOM    137  N   GLN    58      21.344  12.453  16.140  1.00  0.00              
ATOM    138  CA  GLN    58      20.067  12.812  16.740  1.00  0.00              
ATOM    139  C   GLN    58      19.170  11.618  16.980  1.00  0.00              
ATOM    140  O   GLN    58      19.163  10.634  16.249  1.00  0.00              
ATOM    141  N   ARG    59      18.343  11.771  18.008  1.00  0.00              
ATOM    142  CA  ARG    59      17.326  10.762  18.338  1.00  0.00              
ATOM    143  C   ARG    59      16.060  11.145  17.621  1.00  0.00              
ATOM    144  O   ARG    59      15.680  12.357  17.659  1.00  0.00              
ATOM    145  N   LEU    60      15.341  10.211  17.089  1.00  0.00              
ATOM    146  CA  LEU    60      14.101  10.406  16.399  1.00  0.00              
ATOM    147  C   LEU    60      13.093   9.329  16.819  1.00  0.00              
ATOM    148  O   LEU    60      13.473   8.160  16.740  1.00  0.00              
ATOM    149  N   ASN    61      11.896   9.749  17.228  1.00  0.00              
ATOM    150  CA  ASN    61      10.894   8.711  17.573  1.00  0.00              
ATOM    151  C   ASN    61      10.138   8.341  16.312  1.00  0.00              
ATOM    152  O   ASN    61       9.565   9.294  15.664  1.00  0.00              
ATOM    153  N   CYS    62      10.041   7.090  15.937  1.00  0.00              
ATOM    154  CA  CYS    62       9.325   6.703  14.703  1.00  0.00              
ATOM    155  C   CYS    62       8.042   5.974  15.015  1.00  0.00              
ATOM    156  O   CYS    62       7.875   5.377  16.106  1.00  0.00              
ATOM    157  N   SER    80       2.585   4.187  11.658  1.00  0.00              
ATOM    158  CA  SER    80       1.622   4.937  10.825  1.00  0.00              
ATOM    159  C   SER    80       1.762   6.379  11.309  1.00  0.00              
ATOM    160  O   SER    80       1.976   6.593  12.554  1.00  0.00              
ATOM    161  N   ILE    81       1.625   7.339  10.442  1.00  0.00              
ATOM    162  CA  ILE    81       1.721   8.764  10.885  1.00  0.00              
ATOM    163  C   ILE    81       0.888   9.606   9.951  1.00  0.00              
ATOM    164  O   ILE    81       0.501   9.155   8.871  1.00  0.00              
ATOM    165  N   ILE    82       0.574  10.833  10.371  1.00  0.00              
ATOM    166  CA  ILE    82      -0.144  11.803   9.553  1.00  0.00              
ATOM    167  C   ILE    82       0.975  12.602   8.856  1.00  0.00              
ATOM    168  O   ILE    82       1.848  13.203   9.490  1.00  0.00              
ATOM    169  N   CYS    83       0.934  12.507   7.532  1.00  0.00              
ATOM    170  CA  CYS    83       1.996  13.196   6.767  1.00  0.00              
ATOM    171  C   CYS    83       1.579  14.628   6.421  1.00  0.00              
ATOM    172  O   CYS    83       0.373  14.838   6.193  1.00  0.00              
ATOM    173  N   TYR    84       2.581  15.513   6.440  1.00  0.00              
ATOM    174  CA  TYR    84       2.352  16.906   5.990  1.00  0.00              
ATOM    175  C   TYR    84       3.254  17.070   4.711  1.00  0.00              
ATOM    176  O   TYR    84       4.289  16.356   4.685  1.00  0.00              
ATOM    177  N   GLY    85       2.758  17.866   3.781  1.00  0.00              
ATOM    178  CA  GLY    85       3.548  18.090   2.521  1.00  0.00              
ATOM    179  C   GLY    85       3.809  19.558   2.284  1.00  0.00              
ATOM    180  O   GLY    85       3.049  20.443   2.723  1.00  0.00              
ATOM    181  N   GLY    88       1.122  21.388   5.022  1.00  0.00              
ATOM    182  CA  GLY    88      -0.292  21.089   4.779  1.00  0.00              
ATOM    183  C   GLY    88      -0.525  19.615   5.060  1.00  0.00              
ATOM    184  O   GLY    88       0.157  18.733   4.482  1.00  0.00              
ATOM    185  N   SER    89      -1.545  19.266   5.836  1.00  0.00              
ATOM    186  CA  SER    89      -1.883  17.866   6.095  1.00  0.00              
ATOM    187  C   SER    89      -2.320  17.173   4.820  1.00  0.00              
ATOM    188  O   SER    89      -3.103  17.653   3.976  1.00  0.00              
ATOM    189  N   PHE    90      -1.773  15.975   4.651  1.00  0.00              
ATOM    190  CA  PHE    90      -2.110  15.126   3.511  1.00  0.00              
ATOM    191  C   PHE    90      -2.963  13.949   3.920  1.00  0.00              
ATOM    192  O   PHE    90      -3.973  13.626   3.263  1.00  0.00              
ATOM    193  N   SER    91      -2.610  13.285   4.989  1.00  0.00              
ATOM    194  CA  SER    91      -3.420  12.073   5.337  1.00  0.00              
ATOM    195  C   SER    91      -2.494  11.046   5.956  1.00  0.00              
ATOM    196  O   SER    91      -1.314  11.305   6.294  1.00  0.00              
ATOM    197  N   ASN    92      -3.056   9.862   6.211  1.00  0.00              
ATOM    198  CA  ASN    92      -2.332   8.839   6.905  1.00  0.00              
ATOM    199  C   ASN    92      -1.390   8.064   6.016  1.00  0.00              
ATOM    200  O   ASN    92      -1.823   7.723   4.884  1.00  0.00              
ATOM    201  N   CYS    93      -0.240   7.744   6.511  1.00  0.00              
ATOM    202  CA  CYS    93       0.763   6.920   5.859  1.00  0.00              
ATOM    203  C   CYS    93       0.976   5.686   6.767  1.00  0.00              
ATOM    204  O   CYS    93       1.285   5.843   7.944  1.00  0.00              
ATOM    205  N   SER    94       0.881   4.485   6.215  1.00  0.00              
ATOM    206  CA  SER    94       1.096   3.255   7.003  1.00  0.00              
ATOM    207  C   SER    94       2.410   2.666   6.508  1.00  0.00              
ATOM    208  O   SER    94       2.444   2.253   5.296  1.00  0.00              
ATOM    209  N   MET   100       8.871   3.654   4.156  1.00  0.00              
ATOM    210  CA  MET   100       9.150   4.940   4.827  1.00  0.00              
ATOM    211  C   MET   100      10.626   5.061   5.109  1.00  0.00              
ATOM    212  O   MET   100      11.345   3.984   5.022  1.00  0.00              
ATOM    213  N   CYS   101      11.141   6.216   5.390  1.00  0.00              
ATOM    214  CA  CYS   101      12.535   6.387   5.709  1.00  0.00              
ATOM    215  C   CYS   101      12.714   7.325   6.905  1.00  0.00              
ATOM    216  O   CYS   101      11.749   7.993   7.337  1.00  0.00              
ATOM    217  N   HIS   102      13.883   7.360   7.442  1.00  0.00              
ATOM    218  CA  HIS   102      14.337   8.327   8.451  1.00  0.00              
ATOM    219  C   HIS   102      15.583   8.977   7.794  1.00  0.00              
ATOM    220  O   HIS   102      16.395   8.288   7.160  1.00  0.00              
ATOM    221  N   SER   103      15.694  10.314   7.937  1.00  0.00              
ATOM    222  CA  SER   103      16.883  10.907   7.299  1.00  0.00              
ATOM    223  C   SER   103      16.878  12.379   7.625  1.00  0.00              
ATOM    224  O   SER   103      16.140  12.794   8.559  1.00  0.00              
ATOM    225  N   LEU   104      17.681  13.168   6.958  1.00  0.00              
ATOM    226  CA  LEU   104      17.787  14.596   7.187  1.00  0.00              
ATOM    227  C   LEU   104      18.080  15.371   5.908  1.00  0.00              
ATOM    228  O   LEU   104      18.653  14.767   5.004  1.00  0.00              
ATOM    229  N   GLY   105      17.591  16.608   5.878  1.00  0.00              
ATOM    230  CA  GLY   105      17.871  17.390   4.651  1.00  0.00              
ATOM    231  C   GLY   105      17.826  18.858   5.026  1.00  0.00              
ATOM    232  O   GLY   105      17.116  19.266   5.960  1.00  0.00              
END
