Particle-Based Calculation and Visualization of Protein Cavities Using SES Models

The analysis of molecular cavities, where ligands interact with protein structures, plays a critical role in protein structure-based drug design. However, it is a challenge because of the ambiguous definition of the cavity boundaries in most cavity detection methods. The cavities are mostly calculated by input parameters, which are difficult for users to visualize cavities in interactive ways. In this paper, we propose a novel method for the interactive exploration of cavity calculation and visualization. Firstly, the proposed method combines the two solvent-excluded surfaces (SES) models of a given protein to define the boundaries and provides cavity emission points. Secondly, the system provides a user-guided interactive method to allow users to select cavities by simply clicking operations and to track the cavity identify and filling process based on position constraints. Finally, the selected cavities are represented with the colorful depth perception method. Experiments show that our work can effectively identify and calculate cavities.

Authors

• Li Feng Macau University of Science and Technology
• Feng Wang
• Jian Zhang
• Yong Tang South China Normal University
• Jing Zhao
• Lisha Zhou
• Jiayan Wang
• Dongliang Guo
• Amit Kumar Singh

Keywords

• Proteins
• Surface treatment
• Protein engineering
• Probes
• Solvents
• Visualization
• Biological system modeling
• Solvent Accessible Surface Area
• Protein Cavity
• Interactive
• Surface Model
• Depth Perception
• Molecular Modeling
• Protein Molecules
• Undirected
• Effect Of Particles
• Internal Model
• Molecular Surface
• Active Binding Sites
• Collision Detection
• Layer Of Particles
• Cavity Volume
• Grid Nodes
• Probe Radius
• Open Cavity
• Triangular Face
• Outer Model
• Inner Model
• Cavity Region
• Concave Regions
• Smoothed Particle Hydrodynamics
• Cavity Depth
• Cavity Area
• Physical Simulation
• Scanning Direction
• Bounding Box
• Part Of The Molecule
• SES models
• particle system
• protein cavities
• Algorithms
• Humans
• Ligands