Defining and computing accessibility radius

In structural molecular biology software, the accessibility of an atom in a molecule to a ball representing solvent is either computed slowly by building a solventaccessible surface, or estimated quickly by counting neighboring atoms within some radius. We believe that techniques from computational geometry, notably retraction motion planning in Voronoi diagrams, can give a more direct measure that is faster than surface computation. We propose an O(n log n) time algorithm for computing the accessibility radii for sets of points in R2 , and extend this algorithm to sets of circles in R2 and sets of spheres in R3 . We provide results in R3 that approximates accessibility radii from the power diagram.

• Type: Conference
• Year: 2009
• Where: CCCG
• Authors: Vishal Verma, Jack Snoeyink
• Keywords: Accessibility Radii, CCCG 2007, CCCG 2009, Structural Molecular Biology, We Believe