Re: [ccp4bb] BSA

- Protein crystallography

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

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

Next message:
Subject: Re: BSA
From: Eugene Krissinel KEB {- at -} EBI {- dot -} AC {- dot -} UK
Date: 2010-05-26

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

You should take a look at DIFFMODE COMPARE keyword in AREAIMOL manual,
it allows for buried surface area calculation (you have to prepare the
two pdb files with complex and receptor only). If you can easily use
command line and scripts (i.e. you are running CCP4 on non-micro$oft
OS), try the following script. It takes three command line parameters:
the name of the pdb file with complex structure, and two chain IDs (for
receptor and ligand). Notice that if your current directory contains
files named foo1.pdb and foo2.pdb, they will be replaced by the script
and subsequently deleted.

---
#!/usr/bin/env bash
pdbset xyzin $1 xyzout foo2.pdb << eof > /dev/null
select chain $2 $3
eof
pdbset xyzin $1 xyzout foo1.pdb << eof > /dev/null
select chain $2
eof
areaimol xyzin foo2.pdb xyzin2 foo1.pdb << eof

grep 'TOTAL AREA DIFFERENCE'
cut -d: -f 2
DIFFMODE COMPARE
MODE NOHOH
SMODE OFF
REPORT CONTACT YES RESAREA NO
PNTDEN 10
PROBE 1.4
END
eof
rm foo1.pdb
rm foo2.pdb
---

On Wed, 2010-05-26 at 08:45 -0400, Sollepura Yogesha wrote:
> 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

--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /

CCP4bb navigation

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

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

Next message:
Subject: Re: BSA
From: Eugene Krissinel KEB {- at -} EBI {- dot -} AC {- dot -} UK
Date: 2010-05-26