mohsen ramezanpour wrote:
Dear Shahab
Yes,when you compute delta Gibbs energy of binding ,You can compute
binding constant(Kd or Ki)
by thermodynamics relations as Dr.Justin said.
I think both methods can be applied to any systems which you wish to
have its binding free energy.
(including protein-protein,protein-ligand ,protein-Nucleic Asids and
ligand-Nucleic asids)
True, but you will probably get bad convergence for TI with large molecules,
especially those that are not net neutral (like nucleic acids and most
proteins). PMF is much easier in this case, and probably more reliable.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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