Dear All,
I have a metalloprotein (dimer) with docked ligand in the binding site of
one of the monomer. ligand is approx at a distance of 9 angstrom from the
catalytic site of same monomer. Movement of ligand towards the catalytic
site will trigger protein to get close conformation and enzyme catalysis
will take place.
I did classical MD simulation of docked complex but during simulation
ligand is moving out from the binding site.
Will ASMD be appropriate here to calculate PMF for bringing ligand to
active site at a distance of 2-3 angstrom? Or any other method I can do?
Thanks
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Sangita Kachhap
Post Doctoral FellowJerzy Haber Institute of Catalysis and Surface Chemistry
Polish Academy of Sciences
Niezapominajek 8
PL-30239 Krakow, Poland
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Received on Tue Aug 21 2018 - 04:00:03 PDT
