Protein::protein binding is a tremendously hard problem, from a sampling
point of view. The potentials are pretty good, but it sounds almost like a
delta G of folding calculation to bring two proteins into a docked pose and
then pull them apart. I was having a discussion earlier about the extent
of our functionality in Amber, but the CHARMM community has a very clever
method for implementing a harmonic restraint in the contact score (I'd
imagine the algebra is really tedious) to run one-dimensional umbrella
sampling calculations at various degrees of protein folding. You should be
able to leverage that sort of contact score to define bound and unbound
states of your two proteins.
See one of their papers:
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24004/full
Good luck!
Dave
On Thu, Feb 25, 2016 at 1:58 AM, Nhai <nhai.qn.gmail.com> wrote:
> Hi
>
> Please be patient.
>
> Hai
>
> > On Feb 25, 2016, at 1:49 AM, Vertika Gautam <vartikapisces.gmail.com>
> wrote:
> >
> > ---------- Forwarded message ----------
> > From: Vertika Gautam <vartikapisces.gmail.com>
> > Date: Thu, Feb 25, 2016 at 2:44 PM
> > Subject: Thermodynamic Integration
> > To: AMBER Mailing List <amber.ambermd.org>
> >
> >
> > Dear All,
> >
> > I want to compare two Ankyrin proteins (almost similar but one of the
> > Ankyrin with one extra loop) for their binding towards the same receptor.
> > Is it possible to do?
> >
> > PS: for the convinience sequence alignment of two Ankyrins is attached
> > herewith.
> >
> >
> > Thanks
> >
> > --
> > Vertika Gautam
> >
> > Research Assistant
> > Drug Design and Development Research Group (DDDRG)
> > Department of Chemistry, Faculty of Science
> > University of Malaya
> >
> >
> >
> > *e-mail address: vartikapisces.gmail.com
> > <vartikapisces.gmail.com>
> > vartikapisces.hotmail.com <vartikapisces.hotmail.com>
> > 01112294191*
> >
> >
> >
> > --
> > Vertika Gautam
> >
> > Research Assistant
> > Drug Design and Development Research Group (DDDRG)
> > Department of Chemistry, Faculty of Science
> > University of Malaya
> >
> >
> >
> > *e-mail address: vartikapisces.gmail.com
> > <vartikapisces.gmail.com>
> > vartikapisces.hotmail.com <vartikapisces.hotmail.com>
> > 01112294191*
> > <sequence alignment.docx>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 25 2016 - 00:00:04 PST
