On 02/13/2013 04:51 AM, Emmanuel Levy wrote:
> Hello,
>
> I have been looking for a tool to measure the "Protein accessible
> surface area", which could be defined exactly as the solvent ASA
> except with a probe of larger radius.
>
> Most tools that calculate ASA however do not work with a probe radius
> of a size equal to 10 or 50 Angstroms. Plus, ideally one would like to
> know the "largest probe size that can access each atom or residue". So
> using classic ASA programs means one would have to run it ~30 times,
> each time with different probe radius for each protein.
>
> So my question is, do you know of a tool that could help us in
> obtaining this type of information?
Without any guarantee, you may try Voroprot:
http://code.google.com/p/baltymus/wiki/Tutorial
I think it would never crash, whatever the probe size.
> Thanks in advance for any hint,
> All the best,
>
> Emmanuel
>
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