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

From: David A Case <>
Date: Wed, 20 May 2020 13:31:03 -0400

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.


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Received on Wed May 20 2020 - 11:00:01 PDT
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