On 16/07/15 14:04, cedric bauvois wrote:
> Sorry if it was not clear,
>
> Maybe, it will be easier to understand with the example of the
> mechanism of action of b-lactam (probably not the best example but
> well known).
>
> http://proteopedia.org/wiki/index.php/Sandbox_126
> Beta-Lactam (β-Lactam) antibiotics, which include penicillins,
> cephalosporins and carbapenems, bind and irreversibly inhibit
> transpeptidases by mimicking the D-Ala-D-Ala moiety, resulting in the
> inhibition of cell wall synthesis and ultimately bacterial cell growth.
>
> for an illustration in 2D, see
> http://proteopedia.org/wiki/index.php/Image:DalMimic.jpg
>
> In our case, we are working with a small organic compound that mimicks
> a small part of a three turn a-helix peptide and we would be
> interested to find the best way to superimpose them both.
>
> hoping it will help the understanding.
>
>
Yes, it does (for me).
The problem as it stands is tricky because you are matching a single
"residue" onto several - I don't know of any means to do that.
If you can describe your protein fragment as a single "residue" (you
will have to change the atom names for some atoms) then you can use
overlap-ligands and match-ligands-torsion functions in coot. You can
find a clicky-clicky interface for that here:
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/enhanced-ligand.scm
Paul.
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