Linearly Scalable Computation of Smooth Molecular Surfaces
Amitabh Varshney, Frederick P. Brooks, William V. Wright · 1997
An algorithm for fast computation of Richards's smooth molecular surface is described. Our algorithm is easily parallelizable and scales linearly with the number of atoms in a molecule. 1 Introduction The smooth molecular surface of a molecule is de#ned as the surface which an exterior probe-sphere touches as it is rolled over the spherical atoms of that molecule. This de#nition of a molecular surface was #rst proposed by Richards #11#. This surface is useful in studying the structure and interactions of proteins, in particular for attacking the protein-substrate docking problem. For examples of such molecular surfaces, refer to Figures 5 # 10, where these surfaces have been shown for various molecules and with di#erent probe-sphere radii. Present systems for computing the surfaces of molecules are batch-oriented. They take a few minutes to compute the surface for a couple of thousand atoms. Our goal has been to compute and display these surfaces at interactive rates, by taking adva...