REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0077AL009_2 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : XU-YING 
REMARK  ---------------------------------------------------------- 
TARGET T0077  
AUTHOR 4798-1984-8383  
REMARK CASP-3 target T0077, Ribosomal protein L30  
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   
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1ctf 
ATOM      1  N   LEU    14      17.762  15.746 -14.052  1.00  0.00              
ATOM      2  CA  LEU    14      17.509  14.262 -14.184  1.00  0.00              
ATOM      3  C   LEU    14      16.655  13.688 -13.048  1.00  0.00              
ATOM      4  O   LEU    14      16.617  14.260 -11.961  1.00  0.00              
ATOM      5  N   ALA    15      16.142  12.505 -13.309  1.00  0.00              
ATOM      6  CA  ALA    15      15.330  11.738 -12.384  1.00  0.00              
ATOM      7  C   ALA    15      16.106  10.419 -12.018  1.00  0.00              
ATOM      8  O   ALA    15      16.766   9.876 -12.932  1.00  0.00              
ATOM      9  N   LEU    16      15.972   9.986 -10.814  1.00  0.00              
ATOM     10  CA  LEU    16      16.640   8.752 -10.373  1.00  0.00              
ATOM     11  C   LEU    16      15.468   7.830 -10.059  1.00  0.00              
ATOM     12  O   LEU    16      14.647   8.099  -9.142  1.00  0.00              
ATOM     13  N   VAL    17      15.428   6.674 -10.737  1.00  0.00              
ATOM     14  CA  VAL    17      14.361   5.721 -10.503  1.00  0.00              
ATOM     15  C   VAL    17      14.926   4.428  -9.933  1.00  0.00              
ATOM     16  O   VAL    17      15.892   3.898 -10.465  1.00  0.00              
ATOM     17  N   ILE    18      14.296   3.997  -8.885  1.00  0.00              
ATOM     18  CA  ILE    18      14.621   2.726  -8.176  1.00  0.00              
ATOM     19  C   ILE    18      13.793   1.714  -8.964  1.00  0.00              
ATOM     20  O   ILE    18      12.581   1.769  -8.886  1.00  0.00              
ATOM     21  N   LYS    19      14.433   0.897  -9.764  1.00  0.00              
ATOM     22  CA  LYS    19      13.722  -0.100 -10.583  1.00  0.00              
ATOM     23  C   LYS    19      13.448  -1.357  -9.774  1.00  0.00              
ATOM     24  O   LYS    19      12.371  -1.937  -9.930  1.00  0.00              
ATOM     25  N   SER    20      14.292  -1.868  -8.909  1.00  0.00              
ATOM     26  CA  SER    20      14.133  -3.034  -8.084  1.00  0.00              
ATOM     27  C   SER    20      15.167  -3.159  -7.000  1.00  0.00              
ATOM     28  O   SER    20      16.239  -2.706  -7.279  1.00  0.00              
ATOM     29  N   TYR    27      16.949  -5.484  -0.050  1.00  0.00              
ATOM     30  CA  TYR    27      16.107  -4.398   0.515  1.00  0.00              
ATOM     31  C   TYR    27      16.571  -3.716   1.778  1.00  0.00              
ATOM     32  O   TYR    27      16.338  -2.482   1.899  1.00  0.00              
ATOM     33  N   LYS    28      17.161  -4.435   2.702  1.00  0.00              
ATOM     34  CA  LYS    28      17.592  -3.824   3.948  1.00  0.00              
ATOM     35  C   LYS    28      18.629  -2.726   3.685  1.00  0.00              
ATOM     36  O   LYS    28      18.462  -1.567   4.155  1.00  0.00              
ATOM     37  N   SER    29      19.620  -3.087   2.920  1.00  0.00              
ATOM     38  CA  SER    29      20.698  -2.211   2.544  1.00  0.00              
ATOM     39  C   SER    29      20.178  -1.016   1.780  1.00  0.00              
ATOM     40  O   SER    29      20.548   0.144   1.980  1.00  0.00              
ATOM     41  N   THR    30      19.313  -1.255   0.811  1.00  0.00              
ATOM     42  CA  THR    30      18.742  -0.208  -0.025  1.00  0.00              
ATOM     43  C   THR    30      17.892   0.679   0.851  1.00  0.00              
ATOM     44  O   THR    30      18.056   1.913   0.535  1.00  0.00              
ATOM     45  N   VAL    31      17.099   0.203   1.744  1.00  0.00              
ATOM     46  CA  VAL    31      16.291   1.102   2.563  1.00  0.00              
ATOM     47  C   VAL    31      17.166   2.091   3.361  1.00  0.00              
ATOM     48  O   VAL    31      16.906   3.321   3.488  1.00  0.00              
ATOM     49  N   LYS    32      18.292   1.559   3.889  1.00  0.00              
ATOM     50  CA  LYS    32      19.274   2.342   4.627  1.00  0.00              
ATOM     51  C   LYS    32      19.822   3.479   3.706  1.00  0.00              
ATOM     52  O   LYS    32      19.850   4.679   4.141  1.00  0.00              
ATOM     53  N   SER    33      20.250   3.217   2.533  1.00  0.00              
ATOM     54  CA  SER    33      20.821   4.121   1.540  1.00  0.00              
ATOM     55  C   SER    33      19.737   5.163   1.172  1.00  0.00              
ATOM     56  O   SER    33      20.075   6.330   1.104  1.00  0.00              
ATOM     57  N   LEU    34      18.506   4.687   0.920  1.00  0.00              
ATOM     58  CA  LEU    34      17.433   5.677   0.564  1.00  0.00              
ATOM     59  C   LEU    34      17.221   6.621   1.778  1.00  0.00              
ATOM     60  O   LEU    34      17.155   7.873   1.493  1.00  0.00              
ATOM     61  N   ARG    35      17.250   6.244   2.972  1.00  0.00              
ATOM     62  CA  ARG    35      17.064   7.126   4.138  1.00  0.00              
ATOM     63  C   ARG    35      18.218   8.069   4.250  1.00  0.00              
ATOM     64  O   ARG    35      18.072   9.249   4.671  1.00  0.00              
ATOM     65  N   GLN    36      19.429   7.632   3.982  1.00  0.00              
ATOM     66  CA  GLN    36      20.583   8.513   4.093  1.00  0.00              
ATOM     67  C   GLN    36      20.517   9.554   2.975  1.00  0.00              
ATOM     68  O   GLN    36      21.008  10.643   3.231  1.00  0.00              
ATOM     69  N   GLY    37      20.038   9.236   1.831  1.00  0.00              
ATOM     70  CA  GLY    37      20.001  10.145   0.700  1.00  0.00              
ATOM     71  C   GLY    37      18.825  11.092   0.715  1.00  0.00              
ATOM     72  O   GLY    37      19.025  12.188   0.175  1.00  0.00              
ATOM     73  N   LYS    38      17.760  10.705   1.340  1.00  0.00              
ATOM     74  CA  LYS    38      16.513  11.507   1.388  1.00  0.00              
ATOM     75  C   LYS    38      16.032  11.974   2.727  1.00  0.00              
ATOM     76  O   LYS    38      15.180  12.937   2.724  1.00  0.00              
ATOM     77  N   ILE    42      10.044   2.987  -8.622  1.00  0.00              
ATOM     78  CA  ILE    42       9.611   4.312  -8.068  1.00  0.00              
ATOM     79  C   ILE    42      10.598   5.411  -8.366  1.00  0.00              
ATOM     80  O   ILE    42      11.798   5.173  -8.245  1.00  0.00              
ATOM     81  N   ILE    43      10.116   6.602  -8.712  1.00  0.00              
ATOM     82  CA  ILE    43      10.971   7.755  -8.990  1.00  0.00              
ATOM     83  C   ILE    43      11.320   8.276  -7.630  1.00  0.00              
ATOM     84  O   ILE    43      10.497   8.925  -6.967  1.00  0.00              
ATOM     85  N   ILE    44      12.506   8.130  -7.154  1.00  0.00              
ATOM     86  CA  ILE    44      12.969   8.508  -5.861  1.00  0.00              
ATOM     87  C   ILE    44      13.334   9.967  -5.773  1.00  0.00              
ATOM     88  O   ILE    44      12.984  10.537  -4.759  1.00  0.00              
ATOM     89  N   ALA    45      13.965  10.482  -6.729  1.00  0.00              
ATOM     90  CA  ALA    45      14.403  11.899  -6.827  1.00  0.00              
ATOM     91  C   ALA    45      14.199  12.432  -8.202  1.00  0.00              
ATOM     92  O   ALA    45      14.672  11.821  -9.142  1.00  0.00              
ATOM     93  N   ALA    46      13.524  13.597  -8.416  1.00  0.00              
ATOM     94  CA  ALA    46      13.299  14.153  -9.770  1.00  0.00              
ATOM     95  C   ALA    46      13.849  15.613  -9.772  1.00  0.00              
ATOM     96  O   ALA    46      13.957  16.168  -8.699  1.00  0.00              
ATOM     97  N   ASN    47      14.316  16.050 -10.865  1.00  0.00              
ATOM     98  CA  ASN    47      14.905  17.401 -11.016  1.00  0.00              
ATOM     99  C   ASN    47      16.221  17.629 -10.374  1.00  0.00              
ATOM    100  O   ASN    47      16.486  18.774  -9.923  1.00  0.00              
ATOM    101  N   THR    48      17.123  16.622 -10.311  1.00  0.00              
ATOM    102  CA  THR    48      18.453  16.760  -9.713  1.00  0.00              
ATOM    103  C   THR    48      19.421  17.000 -10.924  1.00  0.00              
ATOM    104  O   THR    48      19.173  16.641 -12.050  1.00  0.00              
ATOM    105  N   ARG    52      22.992  16.611 -12.967  1.00  0.00              
ATOM    106  CA  ARG    52      23.724  15.447 -13.446  1.00  0.00              
ATOM    107  C   ARG    52      24.640  14.833 -12.395  1.00  0.00              
ATOM    108  O   ARG    52      24.516  13.576 -12.239  1.00  0.00              
ATOM    109  N   LYS    53      25.431  15.585 -11.642  1.00  0.00              
ATOM    110  CA  LYS    53      26.334  15.044 -10.646  1.00  0.00              
ATOM    111  C   LYS    53      25.576  14.435  -9.484  1.00  0.00              
ATOM    112  O   LYS    53      25.974  13.421  -8.925  1.00  0.00              
ATOM    113  N   SER    54      24.471  15.021  -9.085  1.00  0.00              
ATOM    114  CA  SER    54      23.678  14.531  -7.966  1.00  0.00              
ATOM    115  C   SER    54      23.040  13.170  -8.395  1.00  0.00              
ATOM    116  O   SER    54      23.037  12.335  -7.449  1.00  0.00              
ATOM    117  N   GLU    55      22.592  13.136  -9.598  1.00  0.00              
ATOM    118  CA  GLU    55      21.958  11.895 -10.075  1.00  0.00              
ATOM    119  C   GLU    55      22.928  10.691 -10.188  1.00  0.00              
ATOM    120  O   GLU    55      22.566   9.574  -9.791  1.00  0.00              
ATOM    121  N   LEU    56      24.090  10.970 -10.676  1.00  0.00              
ATOM    122  CA  LEU    56      25.173   9.962 -10.832  1.00  0.00              
ATOM    123  C   LEU    56      25.644   9.572  -9.455  1.00  0.00              
ATOM    124  O   LEU    56      25.831   8.379  -9.200  1.00  0.00              
ATOM    125  N   GLU    57      25.821  10.439  -8.429  1.00  0.00              
ATOM    126  CA  GLU    57      26.213  10.037  -7.103  1.00  0.00              
ATOM    127  C   GLU    57      25.108   9.172  -6.410  1.00  0.00              
ATOM    128  O   GLU    57      25.436   8.227  -5.753  1.00  0.00              
ATOM    129  N   TYR    58      23.820   9.497  -6.519  1.00  0.00              
ATOM    130  CA  TYR    58      22.738   8.769  -5.921  1.00  0.00              
ATOM    131  C   TYR    58      22.656   7.351  -6.635  1.00  0.00              
ATOM    132  O   TYR    58      22.491   6.429  -5.858  1.00  0.00              
ATOM    133  N   TYR    59      22.798   7.335  -7.940  1.00  0.00              
ATOM    134  CA  TYR    59      22.764   6.116  -8.714  1.00  0.00              
ATOM    135  C   TYR    59      23.849   5.148  -8.120  1.00  0.00              
ATOM    136  O   TYR    59      23.626   3.959  -7.855  1.00  0.00              
ATOM    137  N   ALA    60      25.077   5.685  -7.994  1.00  0.00              
ATOM    138  CA  ALA    60      26.165   4.875  -7.480  1.00  0.00              
ATOM    139  C   ALA    60      25.947   4.399  -6.089  1.00  0.00              
ATOM    140  O   ALA    60      26.316   3.205  -5.852  1.00  0.00              
ATOM    141  N   MET    61      25.427   5.266  -5.186  1.00  0.00              
ATOM    142  CA  MET    61      25.152   4.909  -3.819  1.00  0.00              
ATOM    143  C   MET    61      24.073   3.772  -3.857  1.00  0.00              
ATOM    144  O   MET    61      24.287   2.802  -3.072  1.00  0.00              
ATOM    145  N   LEU    62      23.018   3.861  -4.638  1.00  0.00              
ATOM    146  CA  LEU    62      22.009   2.789  -4.605  1.00  0.00              
ATOM    147  C   LEU    62      22.555   1.510  -5.231  1.00  0.00              
ATOM    148  O   LEU    62      22.214   0.490  -4.648  1.00  0.00              
ATOM    149  N   SER    63      23.299   1.706  -6.260  1.00  0.00              
ATOM    150  CA  SER    63      23.971   0.468  -6.903  1.00  0.00              
ATOM    151  C   SER    63      24.844  -0.182  -5.876  1.00  0.00              
ATOM    152  O   SER    63      24.765  -1.388  -5.709  1.00  0.00              
ATOM    153  N   LYS    64      25.680   0.460  -5.097  1.00  0.00              
ATOM    154  CA  LYS    64      26.493  -0.182  -4.081  1.00  0.00              
ATOM    155  C   LYS    64      25.683  -0.822  -2.982  1.00  0.00              
ATOM    156  O   LYS    64      26.148  -1.806  -2.366  1.00  0.00              
ATOM    157  N   THR    65      24.505  -0.298  -2.657  1.00  0.00              
ATOM    158  CA  THR    65      23.619  -0.900  -1.672  1.00  0.00              
ATOM    159  C   THR    65      22.937  -2.118  -2.300  1.00  0.00              
ATOM    160  O   THR    65      22.499  -2.953  -1.482  1.00  0.00              
ATOM    161  N   GLU    76      18.801  -1.983  -8.495  1.00  0.00              
ATOM    162  CA  GLU    76      18.765  -1.821  -9.900  1.00  0.00              
ATOM    163  C   GLU    76      18.188  -0.357 -10.066  1.00  0.00              
ATOM    164  O   GLU    76      17.116  -0.163  -9.605  1.00  0.00              
ATOM    165  N   LEU    77      18.955   0.567 -10.619  1.00  0.00              
ATOM    166  CA  LEU    77      18.540   1.944 -10.734  1.00  0.00              
ATOM    167  C   LEU    77      18.661   2.452 -12.168  1.00  0.00              
ATOM    168  O   LEU    77      19.510   2.031 -12.987  1.00  0.00              
ATOM    169  N   GLY    78      17.858   3.420 -12.460  1.00  0.00              
ATOM    170  CA  GLY    78      17.906   4.068 -13.781  1.00  0.00              
ATOM    171  C   GLY    78      17.957   5.593 -13.612  1.00  0.00              
ATOM    172  O   GLY    78      17.288   6.059 -12.674  1.00  0.00              
ATOM    173  N   THR    79      18.680   6.235 -14.487  1.00  0.00              
ATOM    174  CA  THR    79      18.833   7.754 -14.448  1.00  0.00              
ATOM    175  C   THR    79      18.221   8.166 -15.778  1.00  0.00              
ATOM    176  O   THR    79      18.595   7.627 -16.820  1.00  0.00              
END
