[gmx-users] Re: Active Site

Nuno R. L. Ferreira nunolf at ci.uc.pt
Wed Mar 30 11:21:25 CEST 2005

Hi Wei

About accessible surface ...
I know two programs that do this.
One is from Connolly's, called "msroll". Unfortunaly I think this one is not
free. But it's very good, cause performs a good tesselation.
The other one is "msms", from Sander's.

You didn't told if your active site is solvent exposed ...
Cause if that's not the case, there are a few programs that calculate
internal cavities, and possible their volume. Including Marc's one.
I do not remember the name of them, but a google search would certainly
resolve the problem. Once I used one to scan the protein for cavities, and
if there were any, then it adds water molecules to fill them. I think it was
"solvate" ... but do not know if this one in particular would give the
volume of the cavities.

Have fun.
Best regards,

----- Original Message ----- 
From: "Wei Fu" <fuwei at adrik.bchs.uh.edu>
To: <gmx-users at gromacs.org>
Sent: Tuesday, March 29, 2005 11:57 PM
Subject: [gmx-users] Re: Active Site

> Hi, Nuro,
>     Thanks for your response. You are right, it is important to define the
asscessible surface. I have no idea about it. For my protein, there is a big
active site, it may have several pockets or cavities, but for my case, the
biggest one is active site since the active site of my protein is big.
>     Sure, I will let you know if I figure it out:-)
>                 Wei
>                 2005-03-29
>   Wei Fu (Linda)
>   Postdoctoral Research Associate
>   Department of Biology and Biochemistry
>   University of Houston
>   4800 Calhoun Rd. HSC #402C
>   Houston, TX 77204-5001   USA
>   Phone:713-743-8355(o)  713-741-6388(h)
>   Fax:713-743-8351
>   Email: fuwei at adrik.bchs.uh.edu
>   http://adrik.bchs.uh.edu/~fuwei/
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