AMBER Archive (2009)

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

From: steinbrt_at_rci.rutgers.edu
Date: Sat Aug 22 2009 - 04:50:35 CDT

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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