Protein surface charge density

[Kherim Willems]

Hi,

I would like to calculate the surface charge density of specific sections of a protein (i.e. charge/SASA).

Is it possible to output the solvent accessible surface area in a volumetric format (i.e. amount of surface area present in a volume unit)?

Kind regards,

Kherim

[Nathan Baker]

Hello --

This feature is not currently available in APBS but we would be happy to add it to our list of requested features.

Thanks,

Nathan

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[Kherim Willems]

Hi Nathan,

That would be great! Do you know of any software that can do the same?

Cheers,

Kherim 

[Baker, Nathan]

Hi Kherim –

 

I do not.  However, you might be able to get an estimate by multiplying atomic charge by the solvent-accessible surface area (SASA) associated with each atom.  You can evaluate the per-atom SASA in an APBS APOLAR (http://www.poissonboltzmann.org/docs/apbs-overview/#apolar) calculation with the CALCENERGY COMPS keyword (http://www.poissonboltzmann.org/docs/apbs-overview/#apolarkeywords).

 

Thanks,

 

--

Nathan Baker

Laboratory Fellow and Technical Group Manager

Applied Statistics and Computational Modeling Group

Pacific Northwest National Laboratory

+1-509-375-3997

http://goo.gl/U9xu4t

[Baker, Nathan]

Hi Kherim –

 

I know that Rebecca Wade’s MolSurfer software has provided visualization support for these types of quantities – I’m not sure if she has quantitative output as well.  I’ve Cc’ed her on this email.

 

Thanks,

 

--

Nathan Baker

Laboratory Fellow and Technical Group Manager

Applied Statistics and Computational Modeling Group

Pacific Northwest National Laboratory

+1-509-375-3997

http://goo.gl/U9xu4t

 

 

From: Kherim Willems [mailto:kherim...@gmail.com]
Sent: Monday, January 12, 2015 01:58
To: apbs-...@googlegroups.com
Cc: Baker, Nathan; Jurrus, Elizabeth R; kherim...@gmail.com; Star, Keith; apbs-...@lists.sourceforge.net
Subject: Re: [apbs-users] Protein surface charge density

 

Hi Nathan,