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[ccp4bb] Re-calculating polar/apolar ASA at the interface
 

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CCP4bb <-- 2007 <-- April 2007 <-- 13 April 2007
Previous message:
Subject: Twin refinement with SHELXL
From: "Radisky, Evette S {- dot -} Ph {- dot -} D {- dot -} " Radisky {- dot -} Evette {- at -} MAYO {- dot -} EDU
Date: 2007-04-13 		Next message:
Subject: Research Assistant Position
From: "Meilleur, Flora" meilleurf {- at -} ORNL {- dot -} GOV
Date: 2007-04-15


Subject: Re-calculating polar/apolar ASA at the interface
From: "Ibrahim M {- dot -} Moustafa" I {- dot -} moustafa {- at -} PSU {- dot -} EDU
Date: 2007-04-13
Hi all,

Another solution to calculate the polar vs. non-polar portions of
the ASA at the interface is, as suggested by Susan Crennel,

to use the server: http://www.biochem.ucl.ac.uk/bsm/PP/server/
(actually before posting my question I tried that server which I used
before, but I received no results for the submitted job! now it is working).

The server reports the ASA at the interface for each chain as well
as the % of polar and apolar atoms. The % then can be used to
determine the fractions of polar and non-polar (roughly) for the ASA

at the interface.

Also, Edwin Pozharski suggested the following:

Try Surface Racer or CNS - both programs will give you the output
file with ASA per atom, and you can use that for your polar/apolar
calculation (just add up everything for carbons and rest of the
protein atoms separately - you would need a simple script for that).

Ed.


thanks for all who replied,

Ibrahim
Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
201 Althouse Lab.
University Park, PA16802

Tel (814) 863 8703
Fax (814) 865 7927

CCP4bb navigation

CCP4bb <-- 2007 <-- April 2007 <-- 13 April 2007
Previous message:
Subject: Twin refinement with SHELXL
From: "Radisky, Evette S {- dot -} Ph {- dot -} D {- dot -} " Radisky {- dot -} Evette {- at -} MAYO {- dot -} EDU
Date: 2007-04-13 		Next message:
Subject: Research Assistant Position
From: "Meilleur, Flora" meilleurf {- at -} ORNL {- dot -} GOV
Date: 2007-04-15


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