Thanks Alessandro. In addition to speed, is there any advantage to consider
GBSA over PBSA?
On Tue, Oct 24, 2017 at 8:36 PM, Alessandro Contini <
alessandro.contini.unimi.it> wrote:
> Hi Sangita,
> I'm one of those that reported somehow better results from GBSA than for
> PBSA, but this is contectual to the field of application. In our case
> (http://pubs.acs.org/doi/abs/10.1021/ct400045d or
> http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00196) we were looking
> for a protocol to quickly score several complexes, so speed was quite a
> concern. Indeed, we postprocessed quite short MD trajectories (~4 ns)
> and, being GB more approximated than PB, it also seemed to be less
> sensitive to the MD simulation lenght. Using PB in such approximate
> calculations would have been like using a precision scope on a shotgun
> (it would hardly improve the probability of hitting the target).
>
> All the best,
>
> Alessandro
>
> Il 24/10/2017 16:00, sangita kachhap ha scritto:
> > Thanks for the reply Carlos. I will check these article.
> >
> > On Tue, Oct 24, 2017 at 3:51 PM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> >> I think it's a good idea to do what you mentioned, look at articles that
> >> have tested the methods for performance on problems similar to yours.
> >> However, as a GB developer, my opinion is that GB is really very
> >> approximate and I only use it where speed is most important (such as in
> >> MD). In postprocessing, speed is probably much less important than
> >> accuracy, and in those cases I opt for PB over GB. Also keep in mind
> that
> >> there are many different GB models, and their performance might differ
> for
> >> your problem. For example, when we developed the GBneck2 model in Amber
> >> (igb=8), we optimized for proteins and nucleic acids, but NOT for small
> >> molecule ligands. I would not expect it to perform as well as PB since
> no
> >> data of that type were included in the training or the testing.
> >> carlos
> >>
> >> On Tue, Oct 24, 2017 at 9:47 AM, sangita kachhap <
> nckachap.cyf-kr.edu.pl>
> >> wrote:
> >>
> >>> Dear Amber developer
> >>> I have to compare the binding free energies of different small molecule
> >>> ligands with a protein. According to some of the research article GBSA
> >>> method is good in ranking the free energies of ligands than PBSA. So
> >> which
> >>> method is actually more reliable for comparing the binding free
> energies
> >> of
> >>> ligands.
> >>>
> >>> If difference of binding free energies of two ligands is 5-6 kca/mole.
> >> Are
> >>> these methods able discriminate the such energy difference?
> >>>
> >>> Thanks
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>
> --
> Alessandro Contini, PhD
> Dipartimento di Scienze Farmaceutiche
> Sezione di Chimica Generale e Organica "A. Marchesini"
> Via Venezian, 21 20133 Milano
> tel. +390250314480
> e-mail alessandro.contini.unimi.it
> skype alessandrocontini
>
> http://www.scopus.com/authid/detail.url?authorId=7003441091
> http://orcid.org/0000-0002-4394-8956
> http://www.researcherid.com/rid/F-5064-2012
>
>
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Received on Tue Oct 24 2017 - 13:00:02 PDT
