Plotting Time Series Data From Protein Simulations Using Time Curves

Inspired by a recent paper about Time Curves, I made an interactive visualization to study data derived from protein folding simulations in my research lab. The motive of this project is to understand distributions in variables and correlations between variables that are not apparent in simple line graphs of variables changing over time. This can also be a replacement to watching protein simulation movies where keeping note of several changing variables at the same time can be a formidable task (Sample Protein Simulation video).

Data Source

This data come from a protein simulation - 4 proteins (shown below) in water (not shown).

The size of the protein (radius of gyration), inter-protein distance and other association parameters have been tracked during the simulation.

Visualization Features

Selected data is plotted in a two dimensional space. The location of each point depends on its similarity or dissimilarity with other points. Data points which are similar are grouped together spatially and have the same color. Lines connecting data points show you the flow of time - lighter shades stand for earlier times and darker shades for later. Look out for these interactions:

• Information about each data point as you bring your mouse over
• Paths highlight and show you their direction when you bring your mouse over
• Zoom in and out using the touchpad or scroll keys
• Drag the figure to focus on the areas of interest
• Radio buttons to select number of variables for plotting
• Drop down menus to select the variables of interest

Variable Descriptions

• Energy - Value for the energy of the whole system (in kJ)
• Coordination - Distance between all four proteins
• SS total - Hydrogen bonding between proteins
• Distance - Distance between two proteins (in Angstrom)
• Radius of Gyration - Length of the protein (in Angstrom)

Interaction legend

• Line Color - Light colors signify early time, and darker colors stand for later times
• Circle Color - Shows points with similar values of variables
• Line on Mouseover - Highlighted with an arrow pointing to the next point in the time series
• Tooltip - On moving mouse over circles it displays the data linked with each point
• Zooming - Scroll or use the touch pad to zoom in and move around the space

Time Curve Visualization

Plot 1 Variable Energy Coordination SS Total Distance between 1 and 2 Distance between 1 and 3 Distance between 1 and 4 Distance between 2 and 3 Distance between 2 and 4 Distance between 3 and 4 Radius of Gyration 1 Radius of Gyration 2 Radius of Gyration 3 Radius of Gyration 4

Plot 2 Variables Energy Coordination SS Total Distance between 1 and 2 Distance between 1 and 3 Distance between 1 and 4 Distance between 2 and 3 Distance between 2 and 4 Distance between 3 and 4 Radius of Gyration 1 Radius of Gyration 2 Radius of Gyration 3 Radius of Gyration 4 Energy Coordination SS Total Distance between 1 and 2 Distance between 1 and 3 Distance between 1 and 4 Distance between 2 and 3 Distance between 2 and 4 Distance between 3 and 4 Radius of Gyration 1 Radius of Gyration 2 Radius of Gyration 3 Radius of Gyration 4

Plot 3 Variables Energy Coordination SS Total Distance between 1 and 2 Distance between 1 and 3 Distance between 1 and 4 Distance between 2 and 3 Distance between 2 and 4 Distance between 3 and 4 Radius of Gyration 1 Radius of Gyration 2 Radius of Gyration 3 Radius of Gyration 4 Energy Coordination SS Total Distance between 1 and 2 Distance between 1 and 3 Distance between 1 and 4 Distance between 2 and 3 Distance between 2 and 4 Distance between 3 and 4 Radius of Gyration 1 Radius of Gyration 2 Radius of Gyration 3 Radius of Gyration 4 Energy Coordination SS Total Distance between 1 and 2 Distance between 1 and 3 Distance between 1 and 4 Distance between 2 and 3 Distance between 2 and 4 Distance between 3 and 4 Radius of Gyration 1 Radius of Gyration 2 Radius of Gyration 3 Radius of Gyration 4