[gmx-users] volume of active site

Marc F. Lensink lensink at scmbb.ulb.ac.be
Tue Mar 29 10:51:04 CEST 2005

On Tue, Mar 29, 2005 at 09:21:40AM +0100, Nuno R. L. Ferreira wrote:
> ----- Original Message ----- 
> From: "Wei Fu" <fuwei at adrik.bchs.uh.edu>
> To: <gmx-users at gromacs.org>
> Sent: Friday, March 25, 2005 6:58 PM
> Subject: [gmx-users] volume of active site
> >    I am intersted in the volume change in active site, could you tell if
> there is some method to monitor the volume of active site? Thanks.
> >
> Well, as I understand the problem, some methods exist to calculate the
> volume of a protein. For example, using Voronoy methods, the occluded
> surface concept, the definition of the accessible surface (Connoly surface),
> ...

i have written a program that - very roughly - calculates the volume
of a cavity in a protein.  it's definitely not perfect, and many
better methods exist, but it may give a good indication of what you're
looking for.  also, it only works if the cavity is not connected to
the solvent phase.


Marc F. Lensink           http://www.biochem.oulu.fi/~lensink/
SCMBB, Université Libre de Bruxelles   lensink at scmbb.ulb.ac.be
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425

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