REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0059AL009_1 
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  1 UNREFINED  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1bdo 
ATOM      1  N   LYS     8       9.011  15.990 -21.016  1.00  0.00              
ATOM      2  CA  LYS     8      10.271  15.683 -20.367  1.00  0.00              
ATOM      3  C   LYS     8       9.983  15.536 -18.878  1.00  0.00              
ATOM      4  O   LYS     8       9.477  16.465 -18.249  1.00  0.00              
ATOM      5  N   VAL     9      10.327  14.389 -18.309  1.00  0.00              
ATOM      6  CA  VAL     9      10.069  14.150 -16.892  1.00  0.00              
ATOM      7  C   VAL     9      11.324  14.320 -16.055  1.00  0.00              
ATOM      8  O   VAL     9      12.361  13.726 -16.347  1.00  0.00              
ATOM      9  N   LEU    10      11.228  15.161 -15.036  1.00  0.00              
ATOM     10  CA  LEU    10      12.322  15.403 -14.116  1.00  0.00              
ATOM     11  C   LEU    10      12.086  14.401 -12.991  1.00  0.00              
ATOM     12  O   LEU    10      11.017  14.387 -12.380  1.00  0.00              
ATOM     13  N   HIS    11      13.076  13.562 -12.729  1.00  0.00              
ATOM     14  CA  HIS    11      12.960  12.526 -11.716  1.00  0.00              
ATOM     15  C   HIS    11      13.821  12.787 -10.502  1.00  0.00              
ATOM     16  O   HIS    11      14.774  13.562 -10.551  1.00  0.00              
ATOM     17  N   GLY    15      13.959  10.285  -0.445  1.00  0.00              
ATOM     18  CA  GLY    15      13.790  11.307   0.565  1.00  0.00              
ATOM     19  C   GLY    15      12.386  11.869   0.562  1.00  0.00              
ATOM     20  O   GLY    15      11.454  11.187   0.166  1.00  0.00              
ATOM     21  N   HIS    16      12.250  13.105   1.025  1.00  0.00              
ATOM     22  CA  HIS    16      10.975  13.802   1.102  1.00  0.00              
ATOM     23  C   HIS    16      10.952  14.993   0.144  1.00  0.00              
ATOM     24  O   HIS    16      11.869  15.820   0.120  1.00  0.00              
ATOM     25  N   ILE    17       9.895  15.048  -0.652  1.00  0.00              
ATOM     26  CA  ILE    17       9.678  16.096  -1.642  1.00  0.00              
ATOM     27  C   ILE    17       9.058  17.351  -1.020  1.00  0.00              
ATOM     28  O   ILE    17       8.111  17.261  -0.238  1.00  0.00              
ATOM     29  N   VAL    18       9.586  18.511  -1.396  1.00  0.00              
ATOM     30  CA  VAL    18       9.100  19.810  -0.937  1.00  0.00              
ATOM     31  C   VAL    18       9.027  20.744  -2.133  1.00  0.00              
ATOM     32  O   VAL    18       9.921  20.750  -2.975  1.00  0.00              
ATOM     33  N   GLU    26       6.856  29.137 -16.953  1.00  0.00              
ATOM     34  CA  GLU    26       7.936  28.857 -17.893  1.00  0.00              
ATOM     35  C   GLU    26       9.189  28.787 -17.040  1.00  0.00              
ATOM     36  O   GLU    26       9.361  29.595 -16.125  1.00  0.00              
ATOM     37  N   VAL    27      10.033  27.799 -17.301  1.00  0.00              
ATOM     38  CA  VAL    27      11.277  27.638 -16.562  1.00  0.00              
ATOM     39  C   VAL    27      12.452  27.592 -17.535  1.00  0.00              
ATOM     40  O   VAL    27      12.290  27.247 -18.711  1.00  0.00              
ATOM     41  N   LYS    31      15.436  26.236 -10.088  1.00  0.00              
ATOM     42  CA  LYS    31      15.108  25.265  -9.053  1.00  0.00              
ATOM     43  C   LYS    31      13.616  24.933  -9.167  1.00  0.00              
ATOM     44  O   LYS    31      12.778  25.823  -9.279  1.00  0.00              
ATOM     45  N   LEU    32      13.296  23.646  -9.168  1.00  0.00              
ATOM     46  CA  LEU    32      11.911  23.202  -9.280  1.00  0.00              
ATOM     47  C   LEU    32      11.346  22.752  -7.942  1.00  0.00              
ATOM     48  O   LEU    32      10.163  22.951  -7.651  1.00  0.00              
ATOM     49  N   ILE    33      12.200  22.143  -7.133  1.00  0.00              
ATOM     50  CA  ILE    33      11.785  21.613  -5.853  1.00  0.00              
ATOM     51  C   ILE    33      13.020  21.170  -5.085  1.00  0.00              
ATOM     52  O   ILE    33      14.152  21.352  -5.543  1.00  0.00              
ATOM     53  N   GLU    34      12.779  20.591  -3.916  1.00  0.00              
ATOM     54  CA  GLU    34      13.819  20.097  -3.038  1.00  0.00              
ATOM     55  C   GLU    34      13.454  18.686  -2.588  1.00  0.00              
ATOM     56  O   GLU    34      12.269  18.376  -2.395  1.00  0.00              
ATOM     57  N   ALA    35      14.449  17.805  -2.531  1.00  0.00              
ATOM     58  CA  ALA    35      14.246  16.459  -2.014  1.00  0.00              
ATOM     59  C   ALA    35      15.191  16.445  -0.828  1.00  0.00              
ATOM     60  O   ALA    35      16.362  16.809  -0.956  1.00  0.00              
ATOM     61  N   GLU    36      14.672  16.036   0.319  1.00  0.00              
ATOM     62  CA  GLU    36      15.421  16.023   1.560  1.00  0.00              
ATOM     63  C   GLU    36      15.523  14.638   2.188  1.00  0.00              
ATOM     64  O   GLU    36      14.585  13.848   2.127  1.00  0.00              
ATOM     65  N   ASP    37      16.685  14.334   2.761  1.00  0.00              
ATOM     66  CA  ASP    37      16.894  13.063   3.454  1.00  0.00              
ATOM     67  C   ASP    37      17.807  13.363   4.629  1.00  0.00              
ATOM     68  O   ASP    37      18.954  13.743   4.428  1.00  0.00              
ATOM     69  N   GLN    42      19.736  16.503   4.536  1.00  0.00              
ATOM     70  CA  GLN    42      20.543  16.676   3.330  1.00  0.00              
ATOM     71  C   GLN    42      19.500  17.148   2.320  1.00  0.00              
ATOM     72  O   GLN    42      18.610  16.387   1.945  1.00  0.00              
ATOM     73  N   MET    43      19.568  18.421   1.948  1.00  0.00              
ATOM     74  CA  MET    43      18.603  19.028   1.028  1.00  0.00              
ATOM     75  C   MET    43      19.120  19.250  -0.389  1.00  0.00              
ATOM     76  O   MET    43      19.929  20.138  -0.637  1.00  0.00              
ATOM     77  N   SER    44      18.596  18.466  -1.318  1.00  0.00              
ATOM     78  CA  SER    44      18.998  18.511  -2.714  1.00  0.00              
ATOM     79  C   SER    44      18.028  19.377  -3.524  1.00  0.00              
ATOM     80  O   SER    44      16.823  19.103  -3.558  1.00  0.00              
ATOM     81  N   ASN    45      18.536  20.468  -4.094  1.00  0.00              
ATOM     82  CA  ASN    45      17.726  21.360  -4.930  1.00  0.00              
ATOM     83  C   ASN    45      17.733  20.814  -6.356  1.00  0.00              
ATOM     84  O   ASN    45      18.780  20.732  -6.992  1.00  0.00              
ATOM     85  N   ILE    46      16.560  20.430  -6.842  1.00  0.00              
ATOM     86  CA  ILE    46      16.407  19.862  -8.175  1.00  0.00              
ATOM     87  C   ILE    46      16.205  20.977  -9.193  1.00  0.00              
ATOM     88  O   ILE    46      15.256  21.742  -9.088  1.00  0.00              
ATOM     89  N   THR    47      17.069  21.041 -10.196  1.00  0.00              
ATOM     90  CA  THR    47      16.983  22.081 -11.216  1.00  0.00              
ATOM     91  C   THR    47      16.499  21.568 -12.561  1.00  0.00              
ATOM     92  O   THR    47      16.635  20.381 -12.874  1.00  0.00              
ATOM     93  N   GLY    53      11.348  25.206 -20.709  1.00  0.00              
ATOM     94  CA  GLY    53      10.018  24.856 -21.174  1.00  0.00              
ATOM     95  C   GLY    53       8.951  25.342 -20.214  1.00  0.00              
ATOM     96  O   GLY    53       9.199  26.226 -19.396  1.00  0.00              
ATOM     97  N   ARG    54       7.763  24.768 -20.316  1.00  0.00              
ATOM     98  CA  ARG    54       6.647  25.134 -19.457  1.00  0.00              
ATOM     99  C   ARG    54       6.309  23.958 -18.540  1.00  0.00              
ATOM    100  O   ARG    54       6.333  22.805 -18.961  1.00  0.00              
ATOM    101  N   VAL    55       6.074  24.250 -17.267  1.00  0.00              
ATOM    102  CA  VAL    55       5.710  23.216 -16.307  1.00  0.00              
ATOM    103  C   VAL    55       4.305  22.731 -16.664  1.00  0.00              
ATOM    104  O   VAL    55       3.336  23.489 -16.602  1.00  0.00              
ATOM    105  N   ALA    56       4.225  21.488 -17.110  1.00  0.00              
ATOM    106  CA  ALA    56       2.980  20.863 -17.513  1.00  0.00              
ATOM    107  C   ALA    56       2.246  20.237 -16.337  1.00  0.00              
ATOM    108  O   ALA    56       1.021  20.312 -16.250  1.00  0.00              
ATOM    109  N   GLN    57       2.994  19.628 -15.427  1.00  0.00              
ATOM    110  CA  GLN    57       2.392  18.977 -14.269  1.00  0.00              
ATOM    111  C   GLN    57       3.410  18.724 -13.162  1.00  0.00              
ATOM    112  O   GLN    57       4.610  18.594 -13.424  1.00  0.00              
ATOM    113  N   LEU    58       2.920  18.703 -11.929  1.00  0.00              
ATOM    114  CA  LEU    58       3.726  18.419 -10.747  1.00  0.00              
ATOM    115  C   LEU    58       3.051  17.152 -10.210  1.00  0.00              
ATOM    116  O   LEU    58       1.866  17.145  -9.882  1.00  0.00              
ATOM    117  N   GLN    60       6.993  11.291   0.632  1.00  0.00              
ATOM    118  CA  GLN    60       8.243  10.580   0.365  1.00  0.00              
ATOM    119  C   GLN    60       8.343  10.187  -1.109  1.00  0.00              
ATOM    120  O   GLN    60       7.336   9.877  -1.743  1.00  0.00              
ATOM    121  N   VAL    61       9.544  10.280  -1.669  1.00  0.00              
ATOM    122  CA  VAL    61       9.775   9.912  -3.061  1.00  0.00              
ATOM    123  C   VAL    61      10.919   8.907  -3.132  1.00  0.00              
ATOM    124  O   VAL    61      11.766   8.864  -2.251  1.00  0.00              
ATOM    125  N   ARG    69       9.124  10.018 -10.873  1.00  0.00              
ATOM    126  CA  ARG    69       8.742  11.226 -11.614  1.00  0.00              
ATOM    127  C   ARG    69       8.237  12.311 -10.665  1.00  0.00              
ATOM    128  O   ARG    69       7.376  12.076  -9.813  1.00  0.00              
ATOM    129  N   PHE    70       8.761  13.511 -10.845  1.00  0.00              
ATOM    130  CA  PHE    70       8.398  14.639 -10.003  1.00  0.00              
ATOM    131  C   PHE    70       7.697  15.764 -10.747  1.00  0.00              
ATOM    132  O   PHE    70       6.647  16.238 -10.317  1.00  0.00              
ATOM    133  N   LEU    71       8.289  16.196 -11.855  1.00  0.00              
ATOM    134  CA  LEU    71       7.758  17.315 -12.623  1.00  0.00              
ATOM    135  C   LEU    71       7.844  17.010 -14.111  1.00  0.00              
ATOM    136  O   LEU    71       8.764  16.336 -14.563  1.00  0.00              
ATOM    137  N   ILE    72       6.846  17.466 -14.853  1.00  0.00              
ATOM    138  CA  ILE    72       6.800  17.287 -16.296  1.00  0.00              
ATOM    139  C   ILE    72       6.942  18.664 -16.945  1.00  0.00              
ATOM    140  O   ILE    72       6.239  19.610 -16.587  1.00  0.00              
ATOM    141  N   LEU    73       7.874  18.774 -17.887  1.00  0.00              
ATOM    142  CA  LEU    73       8.143  20.016 -18.600  1.00  0.00              
ATOM    143  C   LEU    73       7.878  19.781 -20.089  1.00  0.00              
ATOM    144  O   LEU    73       8.357  18.798 -20.658  1.00  0.00              
END
