ADL: To what extent, the smaller grid size leads to the more reliable docking results

mswingle at jaguar1.usouthal.edu mswingle at jaguar1.usouthal.edu
Mon Oct 22 22:52:46 PDT 2007


Hi Lu,

I'm sure that this is not the definitive answer, but.....
I think it would depend upon the correctness/reliability of the receptor model. Models built 
using atomic resolution (<~1.2A) X-ray data might benefit significantly from very tiny grid 
spacing (i.e. "bumpier" interaction maps). OTOH, with 3.5A data, crystallographers only 
have vague tubes of electron density to guide them, so there are bound to be lots of errors 
that a larger grid spacing might be able to mask to some extent. Of course, there's also the 
issue of conformational changes upon ligand binding. Small, subtle changes could probably 
be accommodated with larger grid spacing while larger changes would require explicit 
treatment of receptor flexibility.

Regards,

Mark

----- Original Message -----
From: lu liu <luliucmu at gmail.com>
Date: Monday, October 22, 2007 5:24 pm
Subject: ADL: To what extent,        the smaller grid size leads to the more reliable docking 
results
To: autodock at scripps.edu


> Dear Colleagues,
> 
> I understand the smaller grid size is, the more reliable docking results
> are. The default value is 0.375 Angstrom. My question is "Would grid 
> size of
> 0.2 Angstrom be better than 0.375 for sure, or it depends?"
> 
> Thanks for your help.
> 
> Lu
> ________________________________________________
> --- ADL: AutoDock List  ---  ---


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