Measuring properties of molecular surfaces using ray casting

International Workshop on High Performance Computational Biology (HiCOMB) 2010

Left: Estimating the volume enclosed by a surface using ray casting. As rays intersect the surface, we track the total distance traveled inside the volume. Middle: Approximating a surface with planar patches by back-projecting the ray footprints. Note how the patch size varies with the sampling frequency and surface orientation. Right: The volume of molecule 1g2a computed per pixel. Four cavities have been detected.


Molecular geometric properties, such as volume, exposed surface area, and occurrence of internal cavities, are important inputs to many applications in molecular modeling. In this work we describe a very general and highly efficient approach for the accurate computation of such properties, which is applicable to arbitrary molecular surface models. The technique relies on a high performance ray casting framework that can be easily adapted to the computation of further quantities of interest at interactive speed, even for huge models.

Downloads and links

BibTeX reference

  author = {M. Phillips, I. Georgiev, A. K. Dehof, S. Nickels, L. Marsalek, H.-P. Lenhof, A. Hildebrandt, P. Slusallek},
  title = {Measuring Properties of Molecular Surfaces Using Ray Casting},
  booktitle = {Proceedings of 9th International Workshop on High Performance Computational Biology},
  year = {2010},
  month = {April},
  pages = {1--7},
  ISBN = {978-1-4244-6533-0}