Hi Francois,
I have been using MSMS (Sanner et al., 1996) quite a lot, one feature
that I like about it is the output of per-atom area values, what is
exactly the thing you want. Areas of both the solvent-accessible and the
solvent-excluded surface (SES) are computed and written to a file
(.area) if MSMS is run with the -af switch, while to my knowledge the
numerically calculated triangulated surface files (.vert, .face) are
based on the SES by default.
I seem to recall that I once compiled MSMS from source, but I might be
wrong. Looking onto the MSMS page on the Scripps site,
http://mgltools.scripps.edu/packages/MSMS/ there are apparently only
precompiled binaries by now.
Regards,
Fabio
> Date: Thu, 13 Jan 2011 15:00:54 +0900
> From: Francois Berenger<[log in to unmask]>
> Subject: What is the simplest method to analytically compute the Solvent-Accessible Surface Area of a given atom in a protein?
>
> Hello,
>
> Does someone know some good articles on this particular topic?
>
> I'd like to implement the thing myself, however if there is
> a good software doing the job (with readable source code),
> I might use and cite it.
>
> Best regards,
> Francois.
>
> ------------------------------
>
> Date: Wed, 12 Jan 2011 22:30:55 -0800
> From: Pavel Afonine<[log in to unmask]>
> Subject: Re: What is the simplest method to analytically compute the Solvent-Accessible Surface Area of a given atom in a protein?
>
> Bulk-solvent mask calculation (if that's what you want) is available in
> CCTBX library, and it can be easily used. Let me know if interested and we
> can discuss it off-list. I can send you some ten-line Python script-example
> that computes it given a PDB file.
> Pavel.
>
>
> On Wed, Jan 12, 2011 at 10:00 PM, Francois Berenger<[log in to unmask]>wrote:
>
> ------------------------------
>
> Date: Thu, 13 Jan 2011 10:55:51 +0100
> From: Tim Gruene<[log in to unmask]>
> Subject: Re: What is the simplest method to analytically compute the Solvent-Accessible Surface Area of a given atom in a protein?
>
> Dear Francois,
>
> my starting point would be 'man areaimol' which also contains the references
> REFERENCES
>
> 1. B.Lee and F.M.Richards, J.Mol.Biol., 55, 379-400 (1971)
> 2. E.B.Saff and A.B.J.Kuijlaars, The Mathematical Intelligencer, 19,
> 5-11 (1997)
> http://www.math.vanderbilt.edu/~esaff/texts/161.pdf
>
> Cheers, Tim
>
>
--
Dr. rer. nat. Fabio Dall'Antonia
European Molecular Biology Laboratory c/o DESY
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D-22603 Hamburg
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