Re: [AMBER] how to compute the protein interaction surface with the ligand

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Wed, 20 May 2020 15:43:24 -0400

Thomas - what surfaces do you mean by "these two surfaces"?

On Wed, May 20, 2020 at 2:27 PM Thomas Evangelidis <tevang3.gmail.com>
wrote:

> Thanks, but according to PyMOL these two surfaces are not equal, so your
> suggested solution is not valid.
>
> Thomas
>
> Dne st 20. 5. 2020 7:31 PM uĹživatel David A Case <david.case.rutgers.edu>
> napsal:
>
> > On Wed, May 20, 2020, Dan Roe wrote:
> > >>
> > >> I have thousands of PDB files like the attached one and want to
> > calculate
> > >> the surface of the protein atoms that interact with the ligand.
> >
> > To expand on what Dan said: here's a possible algorithm:
> >
> > compute surface areas of protein, ligand, and complex (=protein +
> > ligand)
> >
> > interaction surface area = (protein + ligand - complex)/2
> >
> > The factor of 2 in the formula comes from the fact that complex
> > formation removes both protein surface that contacts the ligand, and
> > ligand surface that contacts the protein. Assuming that these last two
> > are equal gives the factor of 2.
> >
> > Above is clearly approximate, but actually trying to carefully define
> > exactly what you mean by "surface of the protein atoms that interact
> > with ligand" is also fraught with difficulties -- it's not always easy
> > to associate a patch of surface with a given atom.
> >
> > The formula above is well-defined, but may or may not be what you
> > really want.
> >
> > ....dac
> >
> >
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Received on Wed May 20 2020 - 13:00:02 PDT
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