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

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Sun, 24 May 2020 01:32:54 +0200

Carlos- it's clear from the context, as DAC described it: "the protein
surface that contacts the ligand, and
ligand surface that contacts the protein". We have discussed it extensively
in PyMOL's mailing list. Here is the thread:

https://sourceforge.net/p/pymol/mailman/message/37015904/


On Wed, 20 May 2020 at 21:44, Carlos Simmerling <carlos.simmerling.gmail.com>
wrote:

> 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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-- 
======================================================================
Dr. Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>, Prague,
Czech Republic
  &
CEITEC - Central European Institute of Technology
<https://www.ceitec.eu/>, Brno,
Czech Republic
email: tevang3.gmail.com, Twitter: tevangelidis
<https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis
<https://www.linkedin.com/in/thomas-evangelidis-495b45125/>
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Received on Sat May 23 2020 - 17:00:02 PDT
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