Download Interactive Collision Detection for Molecular Graphics

Table of Contents
1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
2 Molecular Docking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2.1 The Docking Task
2.2 Atomic Forces
2.2.1 Trade-offs Between Force Approximations
2.2.2 Non-bonded Atomic Forces
2.2.3 Bond Motion and Internal Vibration
2.3 Previous Docking Systems
3 Collision Detection Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . 5
3.1 Categories of Collision Detection Algorithms
3.2 Grids and Octrees
3.3 BSP-trees and Bounding Volume Hierarchies
3.4 Sweep Algorithms
3.5 Relation Between Collision Detection and Ray Tracing
4 The Bump System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
4.1 User Interface
4.2 A Hypothetical User Session
4.3 Depth Cues
4.3.1 Rocking
4.3.2 Stereo display
4.3.3 Transparency
4.3.4 Shadows
4.3.5 Other Depth Cues
5 Collision Detection in Bump . . . . . . . . . . . . . . . . . . . . . . . . . . 12
5.1 The Bump System
5.2 Uniform Spatial Subdivision
5.3 Collision Along Path of Motion
5.4 Algorithm Performance
6 A User Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
6.1 A Simple Task of Geometric Fit
6.2 User Comments
7 Future Work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
7.1 Enhancements for Molecular Docking
7.2 Interactive Physical Simulation