For example, I know that SWISS PDB allows amino acids to be mutated via substitution and I believe it does have software to allow for energy minimization however rather than the substitution is it possible to remove the amino acid entirely?
Hi Lisa: You can try using MODELLER (https://salilab.org/modeller/) or Chimera https://www.cgl.ucsf.edu/chimera/ or Rosetta https://www.rosettacommons.org/software.
Rachelle
Hi Lisa,
you could also try using phyre2. It is a simple to use online server where you submit a sequence and it will identify templates to use for the modelling. It uses a different algorithm (poing) for the modelling than standard energy minimisation techniques. If you want true energy minimisation then I would also use modeller or the Swiss model server, however there are people out there that would argue that energy minimisation will take your model further away from the true structure and therefore the phyre2 server may be a better choice.
As with all and any models that you produce you have to take with a pinch of salt so to say. These are not true structures and are only possibilities of what the protein could potentially look like. Given that all the techniques suggested here are easy and quick to use you could try them all and compare your resulting models.
Good luck,
James
pymol http://pymol.org/educational/ is another option as well.
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