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

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Wed, 20 May 2020 20:26:48 +0200

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 - 11:30:01 PDT
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