Thank you for the replies.
I have started working on PBSA calculations.
Even after running PBSA, is it meaningful to compare the binding energies
of DNA and RNA with a common receptor (protein) ?
On Tue, Jun 23, 2015 at 5:19 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I agree with Vlad, I think that using PBSA for postprocessing makes sense
> for systems like this. We recently developed a GB model for nucleic acids,
> but this really is intended for MD where PB would be very slow. Since speed
> isn't as important in your binding affinity calculation, you should
> probably use a more accurate model than GB, especially for nucleic acids.
>
> On Tue, Jun 23, 2015 at 7:32 AM, Vlad Cojocaru <
> vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>
> > We had quite poor experiences with MMGBSA for protein-nucleic acids
> > interactions not only because we got completely unrealistic absolute
> > binding free energies but also because of rather poor agreement with
> > experiment of relative dGs. Therefore, we use MMPBSA.
> >
> > For the protocol we use see the paper by Merino et al. in Structure 2014
> > (Structural basis for the SOX dependent redistribution of OCT4 ...) .
> > Although in the paper we focus mostly on DNA-mediated protein-protein
> > interactions, we did play with the protocol to optimize as much as
> possible
> > the protein-DNA energies.
> >
> > A word of caution: multiple tests with the PBSA parameters beyond those
> > specified via MMPBSA.py is required.
> >
> > We are also preparing a follow up study with more discussion on the
> > influence of the PBSA parameters on the results.
> >
> > Hope this helps
> > Vlad
> >
> >
> >
> > On June 23, 2015 12:32:15 PM CEST, Muthukumaran R <kumaran.bicpu.edu.in>
> > wrote:
> > >Dear amber users,
> > >I found from literature and mailing list that implicit simulations for
> > >nucleic acids is not properly parameterized. I have done explicit
> > >solvent
> > >simulations for protein-DNA and protein-RNA complexes. I want to study
> > >the
> > >specificity of protien towards DNA/RNA, in this regard I have performed
> > >binding energy calculations using mmgbsa (AMBER 12 and Amber tools 13)
> > >
> > >Input used:
> > > &general
> > > startframe=20000, endframe=25000,interval=50,
> > > verbose=2, keep_files=1,
> > > /
> > > &gb
> > > igb=5,
> > >
> > >Queries
> > >
> > >1. is it possible to study specificity using MM-GBSA.
> > >2. As it is a relative method, is it meaningful to compare the binding
> > >energies of DNA and RNA?
> > >3. In regard to the gb model, I have adopted igb=5 (modified OBC model)
> > >as
> > >used in "A Computational Study of Nucleosomal DNA Flexibility by Jory
> > >Z.
> > >Ruscio and Alexey Onufriev". is this still an accepted model for
> > >studying
> > >nucleic acids.
> > >
> > >
> > >Apart from MM-GBSA, is there any other analysis/method for studying the
> > >specificity of Protein towards DNA and RNA.??
> > >_______________________________________________
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> >
> > --
> > Sent from my Android device with K-9 Mail. Please excuse my brevity.
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> >
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Received on Tue Jun 23 2015 - 09:30:02 PDT
