Q:

I’m analyzing protein structures (specifically, I’m performing a Voronoi-based analysis) using the tools linked on the geometry page:

http://geometry.molmovdb.org/NucProt/

I’m hoping to run the calculations using just the CA atoms, and so I must change the radii accordingly. Where should I start in terms of figuring out the new radii that should be used?

A:
The most recent re-parameterization of the radii is from Neil Voss’s work about ten years ago. See

http://papers.gersteinlab.org/papers/nucprot/

The logic in this paper could be easily extended to derive a set of CA radii.