Re: [AMBER] selecting the best docking pose with MM/PBSA

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Tue, 9 Dec 2014 15:55:14 -0800

Thomas,

The effect of charges at the binding site is a known issue for mmpbsa.
For one reason, there is no polarization considered in the amber or
charmm force fields. That's why many people use a dielectric constant
higher than 1 (~4 or higher) for solute to implicitly consider
polarization.

There is a discussion regarding this in
http://onlinelibrary.wiley.com/doi/10.1002/prot.23018/abstract;jsessionid=009F5343B4F18B84DF5E47959CCDEAD2.f01t03

Here is an example on protein stability estimation without MD:
http://pubs.acs.org/doi/abs/10.1021/jp709660v

The net effect of polarization overall dampens the electrostatic
contribution of charged groups to computed binding affinities.
However, I'm not saying this is a very clean strategy, but it's a
reasonable and temporary strategy to address it.

All the best,
Ray
--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Tue, Dec 9, 2014 at 1:32 PM, Thomas Evangelidis <tevang3.gmail.com> wrote:
> Hi Prof. Luo,
>
> What about net charge? 2 of the tautomers of the ligand have +1 and +2
> charge, respectively. Does this have a negative impact on binding free
> energy predictions? This paper for instance states that charges at the
> binding interface impair the GB model predictions:
>
> http://pubs.acs.org/doi/abs/10.1021/jp5015934
>
> thanks,
> Thomas
>
>
> On 9 December 2014 at 20:54, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>
>> Hi Thomas,
>>
>> JM2C.
>>
>> I theory, the method should work. The practical issue is that these
>> three binding poses maybe interchangeable during MD simulations, so it
>> becomes hard to know for which pose you are computing delta G …
>>
>> However, I would like to point out that there are successes reported
>> for using the energy model (i.e. AMBER/PBSA) in ranking compounds
>> binding to the same receptor when only minimization was used (without
>> averaging over MD snapshots). It can also rank single-point mutant
>> stabilities in a similar manner (i.e. without MD)
>>
>> So I think it's a very good scientific exercise to see whether you can
>> use the energy model to rank your binding poses after minimization.
>> It's also a reasonable direction to explore a short MD that does not
>> cause dramatic binding poses change in this effort.
>>
>> Ray
>> --
>> Ray Luo, Ph.D.
>> Professor,
>> Biochemistry, Molecular Biophysics, Chemical Physics,
>> Chemical and Biomedical Engineering
>> University of California, Irvine, CA 92697-3900
>>
>>
>> On Mon, Dec 8, 2014 at 3:22 PM, Thomas Evangelidis <tevang3.gmail.com>
>> wrote:
>> > Dear AMBER list,
>> >
>> > I have 3 posing docking poses of a compound. Does calculating relative
>> free
>> > energies of binding with MM/PBSA (without the normal mode approximation)
>> > help selecting the predominant one? I know MM/PBSA makes a lot of very
>> > large assumptions and the differences in the final relative free energies
>> > may be within the error of the method. There is also a dependence on the
>> > ligand force field which determines how strained a conformation is in the
>> > protein. I am just curious to know if other people use this methods to
>> > select the best among a few docking poses.
>> >
>> > thanks in advance,
>> > Thomas
>> >
>> >
>> >
>> > --
>> >
>> > ======================================================================
>> >
>> > Thomas Evangelidis
>> >
>> > PhD student
>> > University of Athens
>> > Faculty of Pharmacy
>> > Department of Pharmaceutical Chemistry
>> > Panepistimioupoli-Zografou
>> > 157 71 Athens
>> > GREECE
>> >
>> > email: tevang.pharm.uoa.gr
>> >
>> >           tevang3.gmail.com
>> >
>> >
>> > website: https://sites.google.com/site/thomasevangelidishomepage/
>> >
>> > ===============================================================
>> >
>> > *Physics is the only real science. The rest are just stamp collecting.*
>> >
>> > *- Ernest Rutherford*
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>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang.pharm.uoa.gr
>
>           tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
> ===============================================================
>
> *Physics is the only real science. The rest are just stamp collecting.*
>
> *- Ernest Rutherford*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Dec 09 2014 - 16:00:03 PST
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