I am trying to come up with an algorithm that would differentiate solvent-exposed surface atoms from cavities which can fit water inside. Unfortunately, it seems the Shrake-Rupley algorithm does not make this distinction.
Please read this review:
A review of methods available to estimate solvent-accessible surface areas of soluble proteins in the folded and unfolded states.
They go over different algorithms, including Shrake and Rupley.
NB - PDF is accessible here: https://www.researchgate.net/profile/Md_Hassan3/publication/261217248_A_R...
Hi beneopp, you cross-posted to three additional forums:
This is typically not recommended as it runs the risk of annoying people in all communities.
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