
PFRMAT ABF1
TARGET T0004
AUTHOR 5865-8356-4011 ANDRAS ASZODI, NIMR, a-aszodi@nimr.mrc.ac.uk
AUTHOR 5865-8356-4011 ROBIN E. J. MUNRO, NIMR, r-munro@nimr.mrc.ac.uk
AUTHOR 5865-8356-4011 WILLIAM R. TAYLOR, NIMR, w_taylor@nimr.mrc.ac.uk
REMARK
REMARK -------------- METHOD DESCRIPTION -------------------
REMARK
REMARK 1) MULTIPLE ALIGNMENT
REMARK The target sequence was aligned to the following homologous
REMARK sequences (SwissProt codes):
REMARK PNP_PHOLU,PNP_HAEIN,YABR_BACSU,RS1_MYCLE,RS1H_BACSU,
REMARK YHGF_ECOLI,RS1_ECOLI
REMARK using MULTAL [Taylor, W. R., J. Mol. Evol. 28:161 (1988)].
REMARK This step was done by R.E.J.M.
REMARK
REMARK 2) FOLD RECOGNITION
REMARK Threading was carried out using the program THREADER
REMARK [Jones, D. T. et al, Nature 358, 86-89.] The top 100 hits were
REMARK collected and the target plus the homologous sequences were
REMARK aligned against these using a new version of MSAP [Taylor, W. R.,
REMARK J. Mol. Biol., submitted]. Three hits were selected manually
REMARK from the MSAP output: chains 1LTSD,1HRHA and 2SNS.
REMARK These steps were done by R.E.J.M. and W.R.T.
REMARK
REMARK 3) FOLD GENERATION
REMARK The results of the MSAP alignments were submitted to DRAGON,
REMARK version 4.16.1 [Aszodi,A. et al., J.Mol.Biol. 251:308 (1995);
REMARK Aszodi,A. and Taylor,W.R., Folding&Design 1:325 (1996)] containing
REMARK the known structures and the target sequence only. 50 models
REMARK were generated for each of the three scaffold structures,
REMARK using C-alpha:C-alpha distances shorter than 10 A to guide
REMARK the folding process. Secondary structure assignments from the
REMARK scaffolds were also mapped onto the target at 30% probability.
REMARK This step was done by A.A.
REMARK
REMARK 4) MODEL BUILDING AND REFINEMENT
REMARK The 10 best-scoring DRAGON output structures were averaged for
REMARK each scaffold. These average structures (C-alpha atoms only)
REMARK constitute the datasets #1,2,3.
REMARK The missing atoms were added to the C-alpha average structures
REMARK and the resulting full-atom structures were minimised by
REMARK QUANTA Version 4.1/CHARMM 23.1. Initial geometry regularisation
REMARK was followed by an in vacuo simulated annealing at T=1000K
REMARK and a second MD run with an 8 A thick solvation layer at T=300 K.
REMARK These refined full-atom models are in the datasets #4,5,6.
REMARK The water molecules' positions are not given.
REMARK This step was done by A.A.
REMARK
REMARK ============== C-alpha TRACE (DRAGON output) =============
REMARK
REMARK Scaffold=2SNS (Staphylococcal nuclease)
REMARK C-alpha RMSD from the average:
REMARK     BEST RMS=1.5484e+00 A
REMARK     WORST RMS=3.0087e+00 A
REMARK     AVERAGE RMS=1.9883e+00 +/- 4.6063e-01 A
BEGDAT 3.1 3 1.0
ATOM      1  CA  ALA     1       9.203  16.601  -5.602  1.00  0.00
ATOM      2  CA  GLU     2       8.566  14.903  -5.118  1.00  0.00
ATOM      3  CA  ILE     3       8.139  13.431  -4.512  1.00  0.00
ATOM      4  CA  GLU     4       9.818  12.555  -5.407  1.00  0.00
ATOM      5  CA  VAL     5      10.948   9.749  -5.618  1.00  0.00
ATOM      6  CA  GLY     6      12.082   8.019  -4.735  1.00  0.00
ATOM      7  CA  ARG     7      10.152   7.964  -2.419  1.00  0.00
ATOM      8  CA  VAL     8       8.096   5.901  -0.920  1.00  0.00
ATOM      9  CA  TYR     9       9.302   3.037  -2.070  1.00  0.00
ATOM     10  CA  THR    10       9.098  -0.121  -2.634  1.00  0.00
ATOM     11  CA  GLY    11       8.803  -2.430   0.241  1.00  0.00
ATOM     12  CA  LYS    12      12.270  -3.291   0.044  1.00  0.00
ATOM     13  CA  VAL    13      12.695  -6.755  -1.033  1.00  0.00
ATOM     14  CA  THR    14      12.233  -8.221   2.395  1.00  0.00
ATOM     15  CA  ARG    15       9.579  -9.052   4.124  1.00  0.00
ATOM     16  CA  ILE    16       6.514  -7.477   3.173  1.00  0.00
ATOM     17  CA  VAL    17       4.218  -7.479   4.594  1.00  0.00
ATOM     18  CA  ASP    18       2.042  -9.510   6.256  1.00  0.00
ATOM     19  CA  PHE    19      -0.198  -7.485   6.553  1.00  0.00
ATOM     20  CA  GLY    20      -1.853  -4.355   6.570  1.00  0.00
ATOM     21  CA  ALA    21       0.890  -2.585   4.469  1.00  0.00
ATOM     22  CA  PHE    22       3.538  -3.126   7.512  1.00  0.00
ATOM     23  CA  VAL    23       6.376  -3.507   5.616  1.00  0.00
ATOM     24  CA  ALA    24       9.279  -2.260   5.090  1.00  0.00
ATOM     25  CA  ILE    25       9.088   0.673   3.397  1.00  0.00
ATOM     26  CA  GLY    26       8.110   3.581   4.408  1.00  0.00
ATOM     27  CA  GLY    27       9.572   4.333   6.788  1.00  0.00
ATOM     28  CA  GLY    28       9.436   1.996   9.099  1.00  0.00
ATOM     29  CA  LYS    29       7.175  -0.518   9.663  1.00  0.00
ATOM     30  CA  GLU    30       4.403   1.033   9.222  1.00  0.00
ATOM     31  CA  GLY    31       2.403   1.454   6.738  1.00  0.00
ATOM     32  CA  LEU    32      -0.737   0.982   6.576  1.00  0.00
ATOM     33  CA  VAL    33      -3.876   1.057   7.369  1.00  0.00
ATOM     34  CA  HIS    34      -6.288  -1.054   6.015  1.00  0.00
ATOM     35  CA  ILE    35      -5.095  -3.843   4.535  1.00  0.00
ATOM     36  CA  SER    36      -3.435  -6.479   5.961  1.00  0.00
ATOM     37  CA  GLN    37      -5.283  -9.320   4.571  1.00  0.00
ATOM     38  CA  ILE    38      -5.474  -9.353   0.890  1.00  0.00
ATOM     39  CA  ALA    39      -2.200  -7.979  -0.325  1.00  0.00
ATOM     40  CA  ASP    40       0.359 -10.573   0.986  1.00  0.00
ATOM     41  CA  LYS    41       0.254 -13.089  -2.009  1.00  0.00
ATOM     42  CA  ARG    42      -0.243 -10.195  -4.747  1.00  0.00
ATOM     43  CA  VAL    43       2.599  -7.912  -3.051  1.00  0.00
ATOM     44  CA  GLU    44       5.502 -10.483  -3.621  1.00  0.00
ATOM     45  CA  LYS    45       5.376 -10.624  -7.430  1.00  0.00
ATOM     46  CA  VAL    46       3.366  -7.362  -8.145  1.00  0.00
ATOM     47  CA  THR    47       6.137  -5.258  -9.649  1.00  0.00
ATOM     48  CA  ASP    48       8.453  -3.871  -6.978  1.00  0.00
ATOM     49  CA  TYR    49       6.383  -2.348  -4.723  1.00  0.00
ATOM     50  CA  LEU    50       4.199  -0.079  -3.629  1.00  0.00
ATOM     51  CA  GLN    51       4.466   3.227  -4.701  1.00  0.00
ATOM     52  CA  MET    52       3.139   5.575  -2.860  1.00  0.00
ATOM     53  CA  GLY    53       3.874   5.303   0.412  1.00  0.00
ATOM     54  CA  GLN    54       5.571   8.593   0.924  1.00  0.00
ATOM     55  CA  GLU    55       3.953   9.280   1.462  1.00  0.00
ATOM     56  CA  VAL    56       1.911   6.850   1.608  1.00  0.00
ATOM     57  CA  PRO    57       1.463   4.929   3.759  1.00  0.00
ATOM     58  CA  VAL    58      -1.202   5.883   5.153  1.00  0.00
ATOM     59  CA  LYS    59      -4.577   5.640   3.992  1.00  0.00
ATOM     60  CA  VAL    60      -5.694   5.249   0.567  1.00  0.00
ATOM     61  CA  LEU    61      -3.512   4.743  -2.414  1.00  0.00
ATOM     62  CA  GLU    62      -1.501   1.904  -1.544  1.00  0.00
ATOM     63  CA  VAL    63      -1.433  -1.626  -1.754  1.00  0.00
ATOM     64  CA  ASP    64      -0.007  -2.306  -5.067  1.00  0.00
ATOM     65  CA  ARG    65      -0.871  -1.448  -8.415  1.00  0.00
ATOM     66  CA  GLN    66      -3.657  -3.550  -8.935  1.00  0.00
ATOM     67  CA  GLY    67      -4.069  -5.301  -5.847  1.00  0.00
ATOM     68  CA  ARG    68      -5.402  -3.157  -3.439  1.00  0.00
ATOM     69  CA  ILE    69      -7.496  -0.213  -3.358  1.00  0.00
ATOM     70  CA  ARG    70     -10.472  -1.194  -5.488  1.00  0.00
ATOM     71  CA  LEU    71     -11.376  -4.482  -3.709  1.00  0.00
ATOM     72  CA  SER    72     -12.245  -2.829  -0.375  1.00  0.00
ATOM     73  CA  ILE    73     -13.825   0.212  -1.689  1.00  0.00
ATOM     74  CA  LYS    74     -16.123  -1.458  -4.181  1.00  0.00
ATOM     75  CA  GLU    75     -18.328  -0.253  -2.632  1.00  0.00
ATOM     76  CA  ALA    76     -15.482   2.731  -2.573  1.00  0.00
ATOM     77  CA  THR    77     -17.710   4.800  -2.866  1.00  0.00
ATOM     78  CA  GLU    78     -19.487   4.610  -0.955  1.00  0.00
ATOM     79  CA  GLN    79     -16.294   3.284   0.110  1.00  0.00
ATOM     80  CA  SER    80     -14.403   5.382  -0.498  1.00  0.00
ATOM     81  CA  GLN    81     -17.083   8.130   0.039  1.00  0.00
ATOM     82  CA  PRO    82     -17.045   6.624   2.193  1.00  0.00
ATOM     83  CA  ALA    83     -13.500   6.222   2.595  1.00  0.00
ATOM     84  CA  ALA    84     -13.560   9.368   2.007  1.00  0.00
ENDDAT 3.1
END
