[Chimera-users] Cavities/Pockets

[Elaine Meng]

Hi George,
In Chimera, I can only think of fairly laborious approaches such as: from the set of atoms or residues identified by CASTp as forming the pocket, sum the surface areas of the nonpolar vs. the polar.  This would give something like a percentage hydrophobicity. You would have to decide on the criterion for polar vs. nonpolar. The Attribute Calculator (under Tools... Structure Analysis) can sum the values for you, but you'd have to use the CASTp info and your polarity criterion to select the appropriate subset of atoms or residues to sum over.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html>

When a molecular surface has been shown, the atoms and residues will automatically have surface area attributes, as explained here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

If you were doing a residue-based calculation, you could use the value of the kdHydrophobicity attribute (Kyte-Doolittle amino acid hydropathy) as the criterion.  
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>

For atoms, one possibility is to consider carbons and their attached hydrogens as nonpolar (can refer to these in the command line as C and HC), the rest polar.  That is fairly crude, however.

If you want something more like a hydrophobic "potential" you would need to use another program, for example the Platinum server:
<http://model.nmr.ru/platinum/>

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 Oct 22, 2011, at 7:49 AM, George Tzotzos wrote:

> I'm wondering if there's a way to work out the relative hydrophobicity of pockets/cavities of related receptors. Fetching CASTp IDs and rendering the surfaces of the cavities gives a crude idea of hydrophobicity of a given cavity. However, I'm looking for something that goes beyond visualisation.
> Any ideas would be most welcome.
> Best regards
> George