Computer simulation using particles
Computer simulation using particles
Combinatorial complexity bounds for arrangements of curves and spheres
Discrete & Computational Geometry - Special issue on the complexity of arrangements
Three-dimensional alpha shapes
ACM Transactions on Graphics (TOG)
Surpassing the information theoretic bound with fusion trees
Journal of Computer and System Sciences - Special issue: papers from the 22nd ACM symposium on the theory of computing, May 14–16, 1990
Spheres, molecules, and hidden surface removal
SCG '94 Proceedings of the tenth annual symposium on Computational geometry
Fast and robust computation of molecular surfaces
Proceedings of the eleventh annual symposium on Computational geometry
Triangulating the surface of a molecule
Discrete Applied Mathematics - Special volume on computational molecular biology
NURBS based B-rep models for macromolecules and their properties
SMA '97 Proceedings of the fourth ACM symposium on Solid modeling and applications
A system for interactive molecular dynamics simulation
I3D '01 Proceedings of the 2001 symposium on Interactive 3D graphics
Computing Smooth Molecular Surfaces
IEEE Computer Graphics and Applications
Dynamic maintenance and visualization of molecular surfaces
Discrete Applied Mathematics - Special issue: Computational molecular biology series issue IV
Fast analytical computation of Richards's smooth molecular surface
VIS '93 Proceedings of the 4th conference on Visualization '93
Journal of Algorithms
On dynamic range reporting in one dimension
Proceedings of the thirty-seventh annual ACM symposium on Theory of computing
Dynamic maintenance of molecular surfaces under conformational changes
SCG '05 Proceedings of the twenty-first annual symposium on Computational geometry
Interactive Protein Manipulation
Proceedings of the 14th IEEE Visualization 2003 (VIS'03)
DockingShop: a Tool for Interactive Protein Docking
CSBW '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference - Workshops
Evolutionary algorithms for automated drug design towards target molecule properties
Proceedings of the 10th annual conference on Genetic and evolutionary computation
Improved maintenance of molecular surfaces using dynamic graph connectivity
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
2009 SIAM/ACM Joint Conference on Geometric and Physical Modeling
Wetting Effects in Hair Simulation
Computer Graphics Forum
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We present the "Dynamic Packing Grid" (DPG) data structure along with details of our implementation and performance results, for maintaining and manipulating flexible molecular models and assemblies. DPG can efficiently maintain the molecular surface (e.g., van der Waals surface and the solvent contact surface) under insertion/deletion/movement (i.e., updates) of atoms or groups of atoms. DPG also permits the fast estimation of important molecular properties (e.g., surface area, volume, polarization energy, etc.) that are needed for computing binding affinities in drug design or in molecular dynamics calculations. DPG can additionally be utilized in efficiently maintaining multiple "rigid" domains of dynamic flexible molecules. In DPG, each up-date takes only O (log w) time w.h.p. on a RAM with w-bit words i.e., O (1) time in practice, and hence is extremely fast. DPG's queries include the reporting of all atoms within O (rmax) distance from any given atom center or point in 3-space in O (log log w) (= O (1)) time w.h.p., where rmax is the radius of the largest atom in the molecule. It can also answer whether a given atom is exposed or buried under the surface within the same time bound, and can return the entire molecular surface in O (m) worst-case time, where m is the number of atoms on the surface. The data structure uses space linear in the number of atoms in the molecule.