[BiO BB] molecular modelling

[Dan Bolser]

On Fri, 21 May 2004 bb2duprm at uco.es wrote:

>I have a question about molecular modelling. I have the 3D structure of
>a protein and I would like to know the effect that one mutation produces
>into that structure. I only have free tools, like Swiss PDB Viwer,
>Modeller, etc. Someone knows how can I do it or what software could I
>use to that purpose? Thank you very much.

You could try YASARA, but chances are you would never see a major change
in structure after changing 1 AA (although the AA may be critical for
folding in vivo).

You could try measuring the energy of the structure before and after the
change (with some minimization) to see if the resulting structure is
'unstable'.

If you are looking at a very specific thing, like a binding site residue,
YASARA should do the job perfectly.

>
>Mario
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