The interaction interface between two molecules can be represented as a bisector surface equidistant from the two sets of spheres of varying radii representing atoms. We recursively divide a box containing both sphere-sets into uniform pairs of sub-boxes. The distance from each new box to each sphere-set is conservatively approximated by an interval, and the number of sphere-box computations is greatly reduced by pre-partitioning each sphere-set using a kd-tree. The subdivision terminates at a specified resolution, creating a box partition (BP) tree. A piecewise linear approximation of the bisector surface is then obtained by traversing the leaves of the BP tree and connecting points equidistant from the sphere-sets. In 124 experiments with up to 16,728 spheres, a bisector surface with a resolution of 124 of the original bounding box was obtained in 28.8 ms on average.
Bibliographical noteFunding Information:
This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology ( 2010-0007785 and 2010-0028106 ) and the Korea Science and Engineering Foundation (KOSEF) grant funded by the Korean government (MEST) ( 2010-0015879 ).
- Interaction interface
- Molecular docking
- Molecule assembly
- Space-partitioning structure
ASJC Scopus subject areas
- Computer Science Applications
- Computer Graphics and Computer-Aided Design
- Industrial and Manufacturing Engineering