[Chimera-users] Castp volume and surface area

[Elaine Meng]

Hi,
The measurement values are fetched from the CASTp database.  I don’t know the precise answer to your question, but you might be misunderstanding the meaning of mouth area.  I believe the mouth area is the surface area of the boundary between inside-pocket space and outside-pocket space, not the surface area of the mouth atoms.  Thus there is no separate “mouth volume,” only inside or outside the pocket.

For a definitive and detailed answer, however, please see the CASTp website and/or literature references:

CASTp website:
<http://sts-fw.bioengr.uic.edu/castp/index.php>

There are a few references, but it looks like this one has the calculation details (click to get the PDF of the whole paper):

Liang,J., Edelsbrunner,H. and Woodward,C. (1998) Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci., 7, 1884–1897.
<http://onlinelibrary.wiley.com/doi/10.1002/pro.5560070905/abstract>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 24, 2014, at 12:41 PM, Felipe Vasquez <anfelvas at gmail.com> wrote:

> Hi,
> I am using CASTp plugin from Chimera in order to calculate both the volume and surface area of a specific pocket. I noticed that the 'mouth' atoms can be excluded from the visualization, and even the surface area is reported separately for both the pocket and the mouths by CASTp. However, there is only one reported volume. Is that volume considering both the pocket and mouth atoms to make just one general calculation? In addition, where can I find more info about the criteria to define a pocket's mouth?
> Thanks in advance for your help.
> Best regards,
> Andrés Felipe Vásquez J., BSc, MSc.
> Grupo de Fisiología Molecular
> Subdirección de Investigación Científica y Tecnológica
> Dirección de Investigación en Salud Pública
> Instituto Nacional de Salud
> Avenida calle 26 No. 51-20 - Zona 6 CAN
> +57 (1) 2207700 ext. 1419
> Bogotá, D.C., Colombia