Subject: CCL: Re:One question about protein-ligand binding

From: Michel Petitjean <ptitjean~at~itodys.jussieu.fr>
Date: Wed, 11 Feb 2004 09:45:35 +0100 (MET)

To: chemistry~at~ccl.net
Subject: CCL: Re:One question about protein-ligand binding

>Baoqiang Cao <caobg~at~email.uc.edu> wrote:
>Dear all,
>
>Are there any ways to quantitatively describe how well a ligand fits a
>protein cavity? Any clues will be welcome!
>Thanks.
>
>Best,
> Cao

If you have the atom-pairs (e.g. H bonds, vdw bonds), a simple criterion
is the variance:
M.Petitjean, Internet Electron J. Mol. Des., 2002,1[4],185-192.
http://www.biochempress.com

Note: a rigorous definition of what is a cavity is difficult. The ALVIS
software offer a simple approach, but it is parametrized by the
radius of the probe.

Michel Petitjean,                     Email: petitjean~at~itodys.jussieu.fr
ITODYS (CNRS, UMR 7086)                      ptitjean~at~ccr.jussieu.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.html
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html