mutate.pl Show Source
mutate.pl [options] [PDBfile]
options: [-seq index:sequence[=index:sequence]]
[-minimize]

This script can be used to mutate residues in an existing protein structure. It requires a continuous single chain structure and will not work if residues are missing.

The input structure is given either as command-line argument or passed through standard input. The option -seq is then used to indicate the new sequence(s) to which the input structure should be mutated. The new sequence is given by the starting residue number where it should replace the original sequence and an abbreviated sequence string. Multiple new sequences can be separated with = in order to mutate different parts of the sequence simultaneously.

Mutations are done by reducing the input structure to a low-resolution model consisting only of C-alpha and side chain center positions and subsequent rebuilding of an all-atom structure with the new sequence. The rebuilding procedure preserves C-alpha coordinates and coordinates from all residues that are not being mutated. This generally results in quite reasonable structures but further force-field minimization may be desirable in order to improve the quality of the models. The flag -minimizeis available to request automatic minimization. The minimization is done with CHARMM using distance dependent dielectric and restraints on the non-mutated parts of the structure and requires a recent version of CHARMM to be installed. If more extensive minimization is needed, the utility minCHARMM.pl may be used.

mutate.pl -seq 10:ADEF 1vii.exp.min.pdb
mutates residues 10 through 13 from VFGM in the original structure to ADEF. 
ATOM      1  N   MET     1       3.075  -9.691  -2.062  0.00  0.000         
ATOM      2  CA  MET     1       1.835  -9.001  -2.351  0.00  0.000         
ATOM      3  C   MET     1       0.889  -9.260  -1.188  0.00  0.000         
ATOM      4  O   MET     1       0.838 -10.371  -0.644  0.00  0.000         
ATOM      5  CB  MET     1       1.181  -9.487  -3.654  0.00  0.000         
ATOM      6  CG  MET     1       1.921  -9.123  -4.938  0.00  0.000         
ATOM      7  SD  MET     1       1.107  -9.774  -6.420  0.00  0.000         
ATOM      8  CE  MET     1       0.002  -8.437  -6.776  0.00  0.000         
ATOM      9  N   LEU     2       0.128  -8.242  -0.786  0.00  0.000         
ATOM     10  CA  LEU     2      -0.806  -8.363   0.321  0.00  0.000         
ATOM     11  C   LEU     2      -2.222  -8.185  -0.206  0.00  0.000         
ATOM     12  O   LEU     2      -2.457  -7.397  -1.132  0.00  0.000         
ATOM     13  CB  LEU     2      -0.566  -7.314   1.412  0.00  0.000         
ATOM     14  CG  LEU     2       0.723  -7.232   2.225  0.00  0.000         
ATOM     15  CD1 LEU     2       1.803  -6.474   1.469  0.00  0.000         
...
mutate.pl -seq 10:ADEF -minimize 1vii.exp.min.pdb
mutates residues and minimizes the resulting structure to relieve unfavorable energetics 
ATOM      1  N   MET     1       3.116  -9.700  -2.114  1.00  0.000     PRO0
ATOM      2  HT1 MET     1       3.622  -9.265  -1.309  1.00  0.000     PRO0
ATOM      3  HT2 MET     1       3.712  -9.622  -2.962  1.00  0.000     PRO0
ATOM      4  HT3 MET     1       2.939 -10.703  -1.903  1.00  0.000     PRO0
ATOM      5  CA  MET     1       1.823  -9.003  -2.332  1.00  0.000     PRO0
ATOM      6  HA  MET     1       2.032  -7.944  -2.370  1.00  0.000     PRO0
ATOM      7  CB  MET     1       1.137  -9.470  -3.642  1.00  0.000     PRO0
ATOM      8  HB1 MET     1       0.149  -8.964  -3.731  1.00  0.000     PRO0
ATOM      9  HB2 MET     1       0.950 -10.566  -3.592  1.00  0.000     PRO0
ATOM     10  CG  MET     1       1.938  -9.167  -4.923  1.00  0.000     PRO0
ATOM     11  HG1 MET     1       2.935  -9.650  -4.831  1.00  0.000     PRO0
ATOM     12  HG2 MET     1       2.108  -8.071  -4.995  1.00  0.000     PRO0
ATOM     13  SD  MET     1       1.136  -9.778  -6.442  1.00  0.000     PRO0
ATOM     14  CE  MET     1      -0.031  -8.411  -6.697  1.00  0.000     PRO0
ATOM     15  HE1 MET     1       0.506  -7.444  -6.805  1.00  0.000     PRO0
...
GenUtil.pm  Molecule.pm  Sequence.pm  SICHO.pm  CHARMM.pm
Michael Feig, Brooks group, TSRI