How to calculate the percent of the buried hydrohobic surface area in a protein with known structure

From: Ke, Jiyuan
Date: 10 November 2011 22:10

Dear All,

 

I have a protein that exists as a dimer in the crystal structure. I want to calculate and compare the area of the buried hydrophobic core of a monomer with that of a dimer? Does anyone know how to do this?  Thanks in advance!

 

Jiyuan Ke, Ph.D.

Research Scientist

Van Andel Research Institute

333 Bostwick Ave NE

Grand Rapids, MI 49503

 

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From: Cale Dakwar

Jiyuan,

I believe PISA will easily do this for you.

C