Buried Protein Atoms vs. Solvent-Accessible Protein Atoms

Question

[beneopp]

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.

[Kevin Blighe]

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...

[h.mon]

Hi beneopp, you cross-posted to three additional forums:

https://bioinformatics.stackexchange.com/questions/4947/

https://biology.stackexchange.com/questions/77013/

https://scicomp.stackexchange.com/questions/30096/

This is typically not recommended as it runs the risk of annoying people in all communities.