AMBER Archive (2009)

Subject: Re: [AMBER] protein-ligand binding simulation times

From: Andrew Voronkov (
Date: Sat Aug 22 2009 - 05:32:42 CDT

Thank you very much for the answer. The task is actually to determine protein-ligand complex stability by molecular dynamics after virtual screening procedure for the best docking scores (to refine 10-50 docking solutions by MD with explicit solvent and to exclude false positives if possible). With the experimental data it's not such a big problem, but there is not only no experimental data, but also one of the tasks is to predict and asses potential binding site for small molecules. This site wasn't reported yet, but seems very likely to be a binding site for some natural ligands and looks like a prospective binding site for small molecule ligands.

Best regards,

22.08.09, 13:50,

> Hi,
> > How much time it will take to assess organic compound's binding with
> > Mw=300-400 to the proteins potential binding site? The goal is to assess
> This is very much an undecided research question. It will take as long as
> your MD needs to sample all relevant conformations of the protein-ligand
> complex that determine the complex stability. Depending on how different
> your starting conformation is from a low energy conformation and how big
> the energetic barriers between states are, this could take anywhere from
> nano- to milliseconds simulated time, or roughly from a few hours to a few
> decades of simulation time.
> Obviously your result will only be approximate in any case, and it can be
> quite hard to even judge how good the approximation is. It always helps if
> you can benchmark result from your specific system with respect to
> experimental data before you start calculations on completely new
> compounds.
> Kind Regards,
> Thomas
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
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