标题: Finding Surface Atoms of a Protein Molecule on a GPU [打印本页] 作者: 彬彬 时间: 2012-1-3 10:14 标题: Finding Surface Atoms of a Protein Molecule on a GPU Copyright is held by the author / owner(s).
SIGGRAPH Asia 2011, Hong Kong, China, December 12 – 15, 2011.
ISBN 978-1-4503-0807-6/11/0012
(a) (b)
Figure 1. An example for PDB ID 1O3Y. (a)a set of sampling
points, (b)surface atoms(red color) and
non-surface atoms(blue color)
1. Introduction
We present a real-time method to find the atoms at the boundary
surface of a protein molecule. Efficient finding of the atoms at the
surface of the molecule is important since most of interactions
between two protein molecules including docking and binding
occur at the boundary surface of molecules.
[Deanda, et al. 2002] proposed a method to extract surface atoms
based on solvent-accessible surfaces. Solvent-accessible surface is
a trajectory of the center of probe solvent, where the solvent
touches the molecule without interference. They defined surface
atoms as the atoms that touch the solvent probes.
We represent the protein molecule as a set of spheres with van der
Waals radii: M = {S(ci, ri)}, where S(ci, ri) is a sphere with center
point ci and radius ri. The probe solvent is represented as a sphere
with radius d. We compute the offset surface of M with offset
distance d. Then, we find the spheres in M, whose d-offset surface
has an intersection with the d-offset surface of M. To achieve the
real-time performance, our algorithm is implemented on a GPU.
2. Algorithm for Finding Surface Atoms
Let us denote the ball with center point c and radius r as B(c, r):
B(c, r) = { p ∈ R3 | ||c – p|| ≤ r }. The surface of B(c, r) is
denoted as a sphere S(c, r): S(c, r) = { p | ||c – p|| = r }. The protein
molecule is represented as follows:
M = { Bi | 0 ≤ i < n },
where Bi = B(ci, ri) corresponds to each atom with center ci and
Van der Waals radius ri. When the radius of given solvent probe is
d, the offset surface of M with offset distance d can be considered
as a boundary surface of Md:
Md = { Bd
i | 0 ≤ i < n },
where Bd
i = B(ci, ri + d) corresponds to the d-offset of Bi. We also
define Sd
i as follows:
Sd
i = S(ci, ri + d).
________________________
* 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(2011-
0004094).
** Corresponding author
When we partition the bounding box of Md into nx × ny × nz voxels,
the bounding box can be represented as a set of voxels as follows:
