[gmx-users] volume of active site

Nuno R. L. Ferreira nunolf at ci.uc.pt
Tue Mar 29 10:21:40 CEST 2005

----- 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

> Hey, all,
>    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.
> Best regards,

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),

But in your case, you want a restricted zone of the protein, the active
site.  The pocket will surely change its volume during the MD runs, since it
belongs to a non-static entity.  But I really do not know if this property
changes a lot, think it depends on the protein and run conditions.

The first problem to resolve I'll guess, its how to define the boundaries of
the active site. Probably, you will need to use the solvent molecules to
establish the outer boundary of the pocket (since its an active site, I'll
expect that its exposed to the solvent).

Then, you could try to calculate the volume of this specific region.
These are only comments. Never done that though.

Best regards,

P.S. If you get around the problem, tell us. Its an interesting concept.
Proteins are a world, aren't they?

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