Paper Citing VMD - Abstract
Seong, Joon-Kyung, Baek, Nakhoon, Kim, Ku-Jin
Real-time approximation of molecular interaction interfaces based on hierarchical space decomposition
COMPUTER-AIDED DESIGN, 43:1598-1605, DEC 2011 2011
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 1/2(4) of the original bounding box was obtained in 28.8 ms on average. (C) 2011 Elsevier Ltd. All rights reserved.