On 10/07/2012 12:02 AM, Boaz Shaanan wrote:
Hi
If you want to calculate the electrostatic properties of your protein/mutants
you can use Delphi or APBS. Calculation of the dielectric constants is most
challenging. I think that these two programs use some approximations to
estimate the variation of dielectric constants between the outside (water with
epsilon = 80 and inside with epsilon = 4 or whatever values you use as input)
but I'm not sure they output those values.
For, APBS, the epsilon values used can be found in the
.in file generated by pdb2pqr if you use it to generate
the file driving APBS.
However, the variation is taken into account when reporting the
electrostatic potential which you can display using PyMol or
UCSF-chimera. As for the hydrophobicity - there are hydrophobicity
scales around (whether you believe them or not is a different matter)
which you can use to display on the surface, again by Pymol or Chimera
(and probably many other programs).
My 2p/2c thoughts.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: [email protected]
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [[email protected]] on behalf of Yarrow Madrona
[[email protected]]
Sent: Saturday, October 06, 2012 4:48 PM
To: [email protected]
Subject: [ccp4bb] calculating dialectric properties of enzyme active site
Hello CCP4 list readers,
Does anyone know how to calculate the dielectric properties of an enzyme
active site? I would like to compare the polarity/hydrophobicity of
similar proteins and different mutants.
Thank you.
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697
