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

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Sat, 23 May 2020 19:45:00 -0400

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.

On Sat, May 23, 2020, 7:33 PM Thomas Evangelidis <tevang3.gmail.com> wrote:

> 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/>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Sat May 23 2020 - 17:00:02 PDT
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