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

From: Thomas Evangelidis <>
Date: Sun, 24 May 2020 02:11:51 +0200

Carlos, the reason I need the interface surface is not directly related to
a physical quantity. I do SQM scoring of compounds bound to proteins, but
the bulkier molecules, which are usually non-binders, tend to yield lower
interaction free energies. Thus, I thought to try the interface surface of
both the protein and the ligand as descriptors (along with others) in a
machine learning-based attempt to balance these pronounced differences and
improve the scoring. I have no idea if this will work out eventually. Maybe
DAC's suggestion, which is actually averaging the sum of the interface
surfaces of the protein and the ligand as computed by PyMOL, will work
better. I will try everything and see.


On Sun, 24 May 2020 at 01:45, Carlos Simmerling <>

> I don't understand the physical concept of 2 separate surfaces with
> different areas for a shared interface. The concept of surface is a
> convenience anyway. Are you talking about a vdw surface? Then maybe one
> could define them separately, though I don't know what meaning one could
> assign to it. I think Dave was talking about the loss of surface area on
> forming the interface, which is what he defined.
Dr. Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <>, Prague,
Czech Republic
CEITEC - Central European Institute of Technology
<>, Brno,
Czech Republic
email:, Twitter: tevangelidis
<>, LinkedIn: Thomas Evangelidis
AMBER mailing list
Received on Sat May 23 2020 - 17:30:02 PDT
Custom Search