3D-Comp

3D-Comp is intended for superposing tertiary structures of two proteins basing on alignment of their primary sequences.

Input data:
PDB file with the structure of protein 1;
PDB file with the structure of protein 2; and
Alignment of these protein sequences.

Output data:
PDB file with superposed structures;
RMSD of C-alpha atoms; and
Location parameters and rotation matrix.

Algorithm:
The method of best superposition of spatial structures independent of their initial positions in the space (Kabsch, 1976) was realized.
Location parameters and rotation matrix are calculated according to C-alpha atoms.

Reference:
Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Cryst. 1976; A32: 922-923.

Program is provided with viewer.

Output example:


HEADER    PROTEIN STRUCTURE ALIGNMENT	
COMPND    (A) file1 chain 1 (B) file2 chain  
REMARK   1
REMARK   1 RMSD on Ca-atoms:  5.446 angstrom
REMARK   1      
REMARK   1      
ATOM      1  N   ARG A   4      -1.746  -1.551 -17.705  1.00 20.00      1TPH 159
ATOM      2  CA  ARG A   4      -2.406  -0.969 -16.527  1.00 18.45      1TPH 160
ATOM      3  C   ARG A   4      -3.056   0.346 -16.901  1.00 17.79      1TPH 161
ATOM      4  O   ARG A   4      -2.402   1.285 -17.394  1.00 16.79      1TPH 162
ATOM      5  CB  ARG A   4      -1.443  -0.773 -15.346  1.00 18.91      1TPH 163
ATOM      6  CG  ARG A   4      -0.782  -2.095 -14.926  1.00 18.65      1TPH 164
ATOM      7  CD  ARG A   4       0.107  -1.913 -13.747  1.00 17.90      1TPH 165
ATOM      8  NE  ARG A   4       1.287  -1.143 -14.064  1.00 18.96      1TPH 166
ATOM      9  CZ  ARG A   4       2.405  -1.563 -14.641  1.00 18.69      1TPH 167
ATOM     10  NH1 ARG A   4       2.536  -2.843 -14.958  1.00 18.24      1TPH 168
ATOM     11  NH2 ARG A   4       3.384  -0.688 -14.913  1.00 19.18      1TPH 169
ATOM     12  N   LYS A   5      -4.354   0.388 -16.624  1.00 16.98      1TPH 170
ATOM     13  CA  LYS A   5      -5.156   1.579 -16.897  1.00 17.05      1TPH 171
ATOM     14  C   LYS A   5      -4.788   2.632 -15.872  1.00 16.14      1TPH 172
ATOM     15  O   LYS A   5      -4.652   2.354 -14.659  1.00 15.95      1TPH 173
ATOM     16  CB  LYS A   5      -6.642   1.226 -16.908  1.00 19.16      1TPH 174
ATOM     17  CG  LYS A   5      -7.534   2.465 -17.082  1.00 20.61      1TPH 175
ATOM     18  CD  LYS A   5      -8.928   2.025 -17.573  1.00 22.50      1TPH 176
ATOM     19  CE  LYS A   5      -9.665   3.236 -18.130  1.00 23.76      1TPH 177
ATOM     20  NZ  LYS A   5     -11.151   2.989 -18.150  1.00 26.08      1TPH 178
ATOM     21  N   PHE A   6      -4.557   3.846 -16.358  1.00 15.28      1TPH 179
ATOM     22  CA  PHE A   6      -4.179   5.021 -15.595  1.00 14.42      1TPH 180
ATOM     23  C   PHE A   6      -5.357   5.270 -14.614  1.00 13.74      1TPH 181
ATOM     24  O   PHE A   6      -6.506   5.243 -15.104  1.00 13.74      1TPH 182
ATOM     25  CB  PHE A   6      -3.896   6.242 -16.480  1.00 15.45      1TPH 183
ATOM     26  CG  PHE A   6      -3.145   7.348 -15.810  1.00 16.58      1TPH 184
ATOM     27  CD1 PHE A   6      -1.848   7.118 -15.336  1.00 17.22      1TPH 185
ATOM     28  CD2 PHE A   6      -3.706   8.602 -15.691  1.00 17.37      1TPH 186
ATOM     29  CE1 PHE A   6      -1.140   8.146 -14.694  1.00 18.11      1TPH 187
ATOM     30  CE2 PHE A   6      -3.017   9.650 -15.076  1.00 18.16      1TPH 188
...
ATOM   1851  CG  HIS A 248      -4.280  13.013 -22.863  1.00 37.01      1TPH2009
ATOM   1852  ND1 HIS A 248      -3.586  11.841 -22.990  1.00 37.77      1TPH2010
ATOM   1853  CD2 HIS A 248      -5.615  12.740 -22.796  1.00 37.69      1TPH2011
ATOM   1854  CE1 HIS A 248      -4.480  10.881 -22.987  1.00 38.21      1TPH2012
ATOM   1855  NE2 HIS A 248      -5.735  11.367 -22.869  1.00 38.19      1TPH2013
ATOM   1856  OXT HIS A 248      -0.450  15.834 -22.118  1.00 35.78      1TPH2014
ATOM      7  N   THR B   1     -12.933  -5.682 -10.516  1.00 40.52      1LAP 103
ATOM      8  CA  THR B   1     -13.050  -4.941  -9.274  1.00 39.43      1LAP 104
ATOM      9  C   THR B   1     -11.679  -4.319  -8.996  1.00 37.36      1LAP 105
ATOM     10  O   THR B   1     -10.702  -4.657  -9.687  1.00 38.20      1LAP 106
ATOM     11  CB  THR B   1     -13.495  -5.968  -8.212  1.00 38.53      1LAP 107
ATOM     12  OG1 THR B   1     -12.792  -7.189  -8.461  1.00 37.44      1LAP 108
ATOM     13  CG2 THR B   1     -14.999  -6.211  -8.275  1.00 39.48      1LAP 109
ATOM     14 1H   THR B   1     -12.541  -5.056 -11.248  1.00 20.00      1LAP 110
ATOM     15 2H   THR B   1     -12.192  -6.364 -10.254  1.00 20.00      1LAP 111
ATOM     16 3H   THR B   1     -13.808  -6.180 -10.765  1.00 20.00      1LAP 112
ATOM     17  HG1 THR B   1     -12.958  -7.792  -7.718  1.00 20.00      1LAP 113
ATOM     21  N   LYS B   2     -11.652  -3.361  -8.089  1.00 30.72      1LAP 114
ATOM     22  CA  LYS B   2     -10.408  -2.765  -7.685  1.00 30.00      1LAP 115
ATOM     23  C   LYS B   2     -10.248  -3.003  -6.195  1.00 28.26      1LAP 116
ATOM     24  O   LYS B   2     -11.216  -3.239  -5.461  1.00 29.56      1LAP 117
ATOM     25  CB  LYS B   2     -10.396  -1.271  -7.916  1.00 29.35      1LAP 118
ATOM     26  CG  LYS B   2     -10.170  -0.836  -9.334  1.00 29.97      1LAP 119
ATOM     27  CD  LYS B   2     -10.243   0.686  -9.378  1.00 32.46      1LAP 120
ATOM     28  CE  LYS B   2     -11.669   1.234  -9.258  1.00 34.49      1LAP 121
ATOM     29  NZ  LYS B   2     -11.710   2.684  -9.110  1.00 34.65      1LAP 122
ATOM     30  H   LYS B   2     -12.450  -3.023  -7.621  1.00 20.00      1LAP 123
...
ATOM   7451  C   GLN B 484      24.036  16.260 -12.472  1.00 47.41      1LAP4582
ATOM   7452  O   GLN B 484      24.945  15.910 -13.247  1.00 51.49      1LAP4583
ATOM   7453  CB  GLN B 484      22.078  15.664 -11.064  1.00 42.25      1LAP4584
ATOM   7454  CG  GLN B 484      21.119  14.544 -10.749  1.00 44.93      1LAP4585
ATOM   7455  CD  GLN B 484      19.652  14.871 -10.669  1.00 45.32      1LAP4586
ATOM   7456  OE1 GLN B 484      18.988  15.253 -11.631  1.00 45.98      1LAP4587
ATOM   7457  NE2 GLN B 484      19.131  14.720  -9.457  1.00 43.27      1LAP4588
ATOM   7458  H   GLN B 484      23.100  13.479 -12.156  1.00 20.00      1LAP4589
ATOM   7459 1HE2 GLN B 484      18.183  14.944  -9.379  1.00 20.00      1LAP4590
ATOM   7460 2HE2 GLN B 484      19.711  14.419  -8.732  1.00 20.00      1LAP4591
TER
END