Hi,
On Fri, Dec 5, 2014 at 3:29 AM, de Manzanos Guinot, Angela
<angela.de-manzanos11.imperial.ac.uk> wrote:
> I am now going to calculate the SASA using LCPO, but I was wondering, what are the main differences in between algorithms? And why some people prefer calculating it with molsurf rather than with LCPO.
The 'molsurf' code calculates the Connolly (also Richards's) surface
area, which is far more accurate than LCPO but also more
temperamental. The algorithm essentially connects sets of curved
regions of geometric shapes (i.e. spheres, torii) to form the surface.
The algorithm is more complex than LCPO and far more accurate (which
is why people prefer it and also why it is slower), but because it is
more complex there are more places where it can fail. You can try
playing around with your probe radius a bit to see if you can get
those frames "working", but I personally don't put much faith in
non-polar terms that are strictly SASA-based since this leaves out
lots of other important stuff like solute volume etc (see e.g. Wagoner
& Baker, PNAS, 2006, 103(22) pp. 8331-8336 or Chandler, Nature, 2005,
437(29) pp.640-647). Not that you shouldn't use it, but it's important
to keep its limitations in mind.
-Dan
>
> Many thanks,
> Angela
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
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Received on Fri Dec 05 2014 - 08:00:02 PST
