## Web Dashboard

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

![](img/compute_1.png)

#### 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.

![](img/compute_2.png)

#### 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

![](img/compute_3.png)

::::{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.

![](img/computation_complete.png)

:::{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.

![](img/view_1.png)

#### 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.

![](img/view_2.png)

#### 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.

![](img/view_3.png)

#### 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.

![](img/view_4.png)

#### 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

![](img/view_5.png)

#### 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

![](img/view_6.png)

#### 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

![](img/view_7.png)