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I am familiar with the Jmol, Rasmol and PyMoL softwares, and was recently introduced to BioBlender. However, I am completely unaware if any of these programs (or others) are capable of loading a .pdb and allowing for the change in a particular amino acid, to ultimately visualize the change in tertiary structure caused by that substitution.

Are any programs capable of performing an amino acid substitution on a molecule loaded by .pdb and showing the change in tertiary structure?

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One application that I am aware of that will do this, as well as much else besides, is Swiss-PDB Viewer aka DeepView. If you go to the site and select User Guide in the left hand tabs you will see a subsection called mutations and following that will tell you what the application can do.

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Visualising the change induced by an amino acid on the 3D structure is part of an entire field of research call molecular modelling (http://en.wikipedia.org/wiki/Molecular_modelling). There is a huge body of research available on the subject and I am not up-to-date anymore in this field.

What I used to do was simulating the optimal shape of a AA chain (~10) which was part of the bigger molecule. The technique consisted in using a Monte-Carlo procedure to simulate heating the molecule and cooling it down millions of time and checking for the stability of the resulting conformation using . I used Modeller, Procheck and Prosa. That was in 2000.

There is a wikipedia list of molecular mechanics modelling software here (http://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling)

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If I understand what you're attempting to accomplish, as David said, this is a vigorous area of study in structural biology. I'll start by saying that a single amino acid substitution will often make virtually no difference in a structure, but there are proteins where a couple substitutions will convert an all alpha-helical protein to all beta-sheet, so I'll leave it to you to judge what's worth trying. There are three routes you can take:

First, for small changes, pymol does have a built in force field ("molecular sculpting") and residue mutagenisis. Chimera has a tool called "minimize structure" that are probably better developed. And VMD has the force field tool kit plugin.

If you expect larger changes, you might go with a full simulation package like NAMD or CHARMM. They would take significant effort to get running, but they're there.

Finally, you can just go with an empirical structure prediction server. All you do is open your sequence file, make your substituions there, upload it to the server, and wait for them to email you the results. They'll do sequence alignments to find relevant PDB files and everything. I recommend the Robetta server (running David Baker's Rosetta). http://robetta.bakerlab.org/

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