[ccp4bb] BSA

- Protein crystallography

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- Protein purification
- Crystallisation

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- Programs for crystallography
- X-ray detectors

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   - Amino Acids

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Structure Based Sequence Alignment
From: Eugene Krissinel KEB {- at -} EBI {- dot -} AC {- dot -} UK
Date: 2010-05-26

Next message:
Subject: Re: BSA
From: Ed Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU
Date: 2010-05-26

Subject: BSA
From: Sollepura Yogesha yogesha {- at -} SCRIPPS {- dot -} EDU
Date: 2010-05-26

Dear All,

I am trying to calculate BSA (Buried surface area) for a protein complex. I am using CCP4 AreaIMol.
I used Accessible surface area module and calculate areas for " protein atoms only"

I know that the buried surface area (BSA) can be calculated as: BSA = ASA(A) + ASA(B) - ASA(AB) when two proteins A and B form a complex AB

So when I run areaIMol for complex AB using AB.pdb, I get
Total area of chain A
Total area of chain A
Total area
Total contact area of chain A
Total contact area of chain A
Total contact area

So,
How do I get my BSA?
Do I need to split PDB in to individual chains to get Accessible surface area for each chain [ ASA(A) and ASA(B)]?
Is the total area I got above is the ASA (AB)?
Are there are any applications which could help get BSA
PISA server giver ASA for each interface and total, so how could I use them to calculate BSA?

Thanks in advance
Yogi

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Structure Based Sequence Alignment
From: Eugene Krissinel KEB {- at -} EBI {- dot -} AC {- dot -} UK
Date: 2010-05-26

Next message:
Subject: Re: BSA
From: Ed Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU
Date: 2010-05-26