I have performed in silico mutation using VMD.
But I need explanation on :
a.) How to manage NTER and CTER? Do we need to change the charge or cap it or do nothing to it? And if we do need to change it why it is so?
b.) After the in-silico mutation, there is changes that happen in pdb file : the TER /ENDMOL will be missing. Is that acceptable if we add back the TER and ENDMOL based on original pdb or do there sny other method to edit it?
c.) Then if pymol or chimera is used there are existence of rotamers. I need help on how to identify or select the rotamers that suits the target protein.
d.) How to do mutation on dimer/ multi chain protein?
e.) If anyone have the reliable methodology to perform the in-silico mutation please share.
Dear Nityanan,
try Triton. very good software for Mutagenesis
http://www.ncbr.muni.cz/triton/
Dear Nityanan,
try Triton. very good software for Mutagenesis
http://www.ncbr.muni.cz/triton/
You definitely need to apply an algorithm which will select the optimal rotamer of the mutated resisude. The golden standard here is SCWRL (http://dunbrack.fccc.edu/SCWRL3.php/), which has been extensively tested.
The answer to all other questions depends on what you want to do next with the proteins. The CTERM/NTERM are usually left intact. The TER/ENDMOL lined are not needed by many programs, and if they are they can be added manually. Mutating dimers is straightfoward, since when mutating you always specify the chain letter/number.
Hi Nithyanan,
How many residues you want to mutate?
I am just adding a few things regarding Chimera, as @Bartosz has already explained thoroughly.
In silico mutation will not drastically change the 3D structure (I hope so). Chimera can be a suitable choice for in silico mutations. During mutation, you can select a particular rotamer based on its probability (given alongside in Chimera). High probability means the chance of one residue in that conformation is dominating over others. So, you can select accordingly. After that, you can perform energy minimisation in Chimera that will remove any unfavourable contacts/clashes.
Mutating single chain molecule is similar to that of multi-chain molecule in chimera. There is a tutorial on youtube about mutation and energy minimization. you can have a look at that one.
HTH,
Ayaz
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