VMD-L Mailing List

From: Luis Guillermo Cota Preciado (lgc_at_mantis.labvis.unam.mx)
Date: Thu May 04 2006 - 12:48:53 CDT

You might want to take a look at the FADE/PADRE software, by Julie
Mitchell (I quote from the site, http://www.sdsc.edu/CCMS/FP/index.html):

"The Fast Atomic Density Evaluator (FADE) and Pairwise Atomic Density
Reverse Engineering (PADRE) programs are designed to aid in the molecular
modeling of proteins. In particular, the programs can rapidly elucidate
features of interest such as crevices, grooves and protrusions. The
topographical information produced by FADE and PADRE can help researchers
easily pinpoint the most prominent features of a protein, regions which
are likely to participate in interactions with other molecules. In
addition to providing shape descriptors to aid in analyzing single
molecules, FADE can directly evaluate the level of shape complementarity
for docked protein-protein complexes."

Best regards from Mexico.

> Wei Fu (Linda) wrote:

>Hello,
>
> Is there any way to display the volume of cavity/pocket/channel of a
protein in VMD? Do I need to install some plugin program or calculate the
volume of cavity by other software, then use VMD to read the map of the
volume?
>
> Best,
>
> Linda
>
> 2006-05-02
>
> 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)
> Fax:713-743-8351
> Email: fuwei_at_adrik.bchs.uh.edu
> http://adrik.bchs.uh.edu/~fuwei/