On 4/14/13 8:54 AM, James Starlight wrote:
Justin,
and what exactly method from that list could be most easily performed in
gromacs for the estimation of the affinity of small mollecules to the
membrane receptors?
There is no universal answer to that question. Explore the literature; there is
a vast amount of information available on such calculations. Proceed with
whatever is feasible and most reasonable for your purposes.
-Justin
2013/4/14 Justin Lemkul <jalem...@vt.edu>
On 4/14/13 2:13 AM, James Starlight wrote:
Dear Gromacs users!
I wounder to know if it possible to simple estimate drug affinity by mean
of MD simulation? As I know the drug's property is based on the free
energy
change of bound-unbound ligand. So It seems that Justin's tutorial (free
energy calculations) might be usefull if it would not be so routine for
the
drugs ( in that workflow several coulombic-vdw interactions must be
uncoupled). Is there any more easily way to perform such calculations for
the typical small-drug compounds consisted of several non-covalent
interactions with the receptors ?
Free energy calculations require considerable effort. You can approach
the task in a number of ways - FEP, BAR, TI, LIE, PMF, MM/PBSA, etc. There
is a large body of literature detailing methods for such calculations.
-Justin
--
==============================**==========
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================**==========
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before
posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read
http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
