Visual Analysis of Dynamic Protein Cavities and Binding Sites

We present a visual analysis application for protein simulations that allows researchers to investigate dynamic data interactively. Special focus lies on the analysis of cavities and binding sites, which play a critical role in protein function. Cavities are extracted and classified. The surface area of all cavities and the diameter of pockets and channels is computed to provide evidence for their accessibility. These values are also plotted in 2D graphs for a quantitative time-dependent analysis. For dynamic simulation data sets, the cavities are tracked to show their stability over time. The user is provided with a range of application-related parameters to interactively adjust the analysis algorithms. A sequence diagram shows the structure of the protein and additional annotations like binding sites. Furthermore, all views support brushing and linking for consistent selection and filtering. All algorithmic steps are implemented to run interactively on a commodity workstation. As a result, the user can immediately see the effect of a parameter change. This enables the real-time analysis of a running simulation for in-situ visualization.