Since several people have asked me for code, I now realize that I've
contributed my bit to the confusion over names of various surface definitions.
To clear things up there is an excellent online article which covers the
history of various molecular surface definitions that I highly recommend:
It can go both ways: If you increase atom radii by adding that of the
probe (e.g. 1.4 A° for a water probe) and calculate the molecular
surface using a zero probe with atom radii as previously defined (Ri
+1.4 A°), the area you get is that of the accessible surface.
Pr. Nadir T. Mrabet
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
Good points Richard!
The ambiguity with surface definition starts with the assumption that
atoms are (i) spheres and (ii) with fixed radii.
I am not sure Connolly was able to sell his original algorithm due to
conflicts of interest with the Scripps, where it had been actually
developped
I'll dig up the code (it's been a long time). It was included in my OpenDX
Chemistry modules package. Interested persons should email me and I'll give
them a temporary password to download from one of our machines.
The ambiguity I was thinking of is that when you have two protein atoms
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)
:
Subject: Re: [ccp4bb] What is the simplest method to analytically compute the
Solvent-Accessible Surface Area of a given atom in a protein?
My knowledge on this is probably quite out of date by now, but some years ago
there was a lot of research on this topic because such surfaces are
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.
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
