Efficient molecular surface rendering by linear-time pseudo-Gaussian approximation to Lee-Richards surfaces (PGALRS).

ABSTRACT: The PGALRS (pseudo-Gaussian approximation to Lee-Richards surfaces) algorithm is discussed. By modeling electron density with unphysical pseudo-Gaussian atoms, the Lee-Richards surface can be approximated by a contour level of that density in time approximately linear in the number of atoms. Having that contour level, the atoms and residues closest to that surface can be identified in average time O[n(2/3)log(n)] using a NearTree-based nearest neighbor search. If a high-quality Lee-Richards surface is required, then, as a final stage, one of the standard Lee-Richards algorithms can be used but considering only the previously identified surface residues; the typical cost is thereby reduced to O[n(2/3)log(n)], making the overall average time for all the steps O(n). For very large macromolecu

SUBMITTER: Bernstein HJ 

PROVIDER: S-EPMC2839470 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature