Web Dashboard

ProLint provides a web-based dashboard for interactive analysis. Access it at https://prolint.ca.

The dashboard has two main pages:

  • Compute Page: Upload files, configure parameters, and run computations

  • View Page: Explore results with interactive visualizations

Compute Page

The Compute page guides you through loading data and running contact computations.

Upload Files

Topology File (required)

Drag and drop or click to upload your topology file. Supported formats include .gro, .pdb, .tpr, .psf, .mol2, and .xyz.

Trajectory File (optional)

For multi-frame analysis, also upload a trajectory: .xtc, .trr, .dcd, or .nc.

After upload, the dashboard displays dataset metadata including number of frames, atoms, and residues.

Configure Parameters

Atom Selections

Use MDAnalysis selection syntax to define what to analyze:

  • Query Selection: Atoms to analyze, set to protein by default

  • Database Selection: Reference atoms for contacts, set to not protein by default

Selection examples:

  • protein — All protein atoms

  • resname POPC POPE CHOL — Specific lipid types

  • resid 1-100 — Specific residue range

Frame Range

  • Start Frame: First frame (0-indexed)

  • End Frame: Last frame (leave empty for all)

  • Step: Frame stride (1 = every frame, 10 = every 10th)

Tip

The dashboard allows a maximum of 5,000 frames per computation. For larger trajectories, adjust the step value to stay within this limit (e.g., for a 50,000 frame trajectory, use step ≥ 10). Start with a higher step to quickly preview results, then reduce it for finer analysis.

Distance Cutoff

Maximum distance (in Ångströms) for detecting contacts. Default is 7.0 Å.

Analyze Replicas

Before running the computation, click the “Analyze Replicas” button to check if your query selection contains multiple copies (replicas) of the same molecule. This step is required before computing contacts.

  • If replicas with overlapping residue IDs are detected, a dropdown will appear allowing you to select which replica to analyze

  • Select the desired replica from the dropdown (e.g., “Replica A”) to proceed

Note

To analyze all replicas together (e.g., for multimer complexes), ensure each replica has unique residue IDs with no overlap in your input files. ProLint will then process them collectively without requiring a replica selection.

Run Computation

Click “Compute Interactions” to start the analysis. A progress indicator shows computation status.

When complete, you’ll see a Result ID and computation time. Click “View Results” to navigate to the View page.

Note

Save your Result ID to return to your results later.

View Page

The View page provides interactive visualizations of your computed contacts.

Database Type Filter

Use the individual buttons to filter results by molecule type. This updates all visualizations.

2D Density Map

Spatial distribution of database molecules around the query structure.

  • 2D view showing where molecules preferentially locate

  • Color intensity indicates density (brighter = more frequent)

Use this to identify enrichment or depletion zones around specific regions of the query.

3D Projection Viewer

Interactive 3D visualization using Mol*.

  • Query structure colored by metric (occupancy, mean contacts, etc.)

  • Rotate, zoom, and pan with mouse controls

  • High and low contact regions highlighted

Controls: Left-click + drag to rotate, right-click + drag to pan, scroll to zoom.

Metric Logo Plot

Sequence-level view of per-residue metrics across the query.

  • Each residue displayed as a single-letter code

  • Color intensity reflects metric value (occupancy, mean duration, etc.)

  • Hover over residues for detailed values

  • Click to select residues for further analysis

Use this to quickly identify hotspots along the sequence.

Shared Contacts Network

Network graph showing which residues contact the same database molecules.

  • Nodes represent query residues

  • Edges indicate shared contacts

  • Edge thickness reflects number of shared contacts

  • Draggable nodes with interactive layout

Use this to identify residue clusters that may form binding sites.

Time Series Plot

Line chart showing how contact counts change over the trajectory.

  • Select individual residues to compare

  • Frame-by-frame contact counts

  • Zoom and pan on time axis

Distance Analysis

Track distances between specific query-database residue pairs over time.

  • Distance plotted frame-by-frame across the trajectory

  • Identify binding and unbinding events

Kinetics Analysis

Detailed binding kinetics for selected residue-molecule pairs.

  • Survival Curve: Probability that a contact persists over time, with exponential fits

  • Residence Time Distribution: Histogram of contact durations

  • Kinetic Parameters: k_on, k_off, mean residence time, occupancy