> ## Documentation Index
> Fetch the complete documentation index at: https://docs.boltz.bio/llms.txt
> Use this file to discover all available pages before exploring further.

# Results & Triage

> Analyze virtual screen results and collaboratively prioritize molecules

## Results Table

Navigating to an **Experiment** shows the results table from all Virtual Screens it contains. The Table UI is divided into three sections: a data table, MolStar viewer, and a progressive flow chart of affinity predictions and RDKit descriptors.

<img src="https://mintcdn.com/boltzpbc/tEZyK9wozfHwPONX/images/image-27.png?fit=max&auto=format&n=tEZyK9wozfHwPONX&q=85&s=0f543e0d9d74d84a98df5819951e993f" alt="Image" width="1901" height="1002" data-path="images/image-27.png" />

### Table Features

| Feature               | Description                                                                                                                |
| --------------------- | -------------------------------------------------------------------------------------------------------------------------- |
| **Selecting a row**   | Loads molecule into the viewer. Clicking the checkbox, multiple (up to 10) molecules can be selected and overlaid.         |
| **ID and Tags**       | Unique ID for the molecule. Click the ⭐ to mark as 'active' in the Catalog. Tags allow labelling with contextual keywords. |
| **Alert Level**       | Indicates if the molecule hits any structural alert filters.                                                               |
| **Triage Elements**   | Upvote/Downvote + Flag buttons for annotation. Connected to the Triage UI.                                                 |
| **Boltz Metrics**     | Metrics for each prediction, grouped by target if multiple exist.                                                          |
| **RDKit Descriptors** | Standard molecular descriptors for triage and analysis.                                                                    |
| **Columns + Sorting** | Toggle columns, drag to rearrange, click headers to sort.                                                                  |
| **Filters**           | Numeric sliders and text/contextual filters available.                                                                     |
| **Download**          | Export all molecules and metrics from the table.                                                                           |

<Tip>
  Results are downsampled to a couple thousand at most for user convienience.\
  \
  Sorting by a column will display to top results, with additional filters then applied to show the highest fidelity hits
</Tip>

<Tip>
  Download will provide an output data file of all molecules in the downsample, or remaining after filters are applied.\
  \
  Selecting molecules will only download the data for those molecules.\
  \
  Please contact support for any additional download requests
</Tip>

***

### Boltz Scoring Metrics

<CardGroup cols={2}>
  <Card title="Binding Confidence" icon="chart-line">
    Primary scoring function for **hit discovery**. Continuous score between 0 and 1, with 1 being highest confidence of binding.

    This is similar to the affinity probability output of Boltz-2.
  </Card>

  <Card title="Optimization Score" icon="chart-line">
    Scoring function for **lead optimization** settings where relative ranking within a series matters. Continuous score between 0 and 1, with 1 being the strongest binder.

    This is similar to the affinity value output of Boltz-2.
  </Card>

  <Card title="Structure Confidence" icon="chart-line">
    Measure of confidence on the correctness of the structure prediction, combines pLDDT and ipTM score.

    Continuous score between 0 and 1, with 1 being highest confidence.
  </Card>
</CardGroup>

### Viewer Features

<Info>
  Note that, for large targets, the model focuses the prediction in the pocket selected in the Target creation stage. If you are looking for the molecules to bind to a different pocket, add a new target. If you are looking to analyze the specific conformational changes on the full target from a ligand binding, use the Sandbox.
</Info>

| Feature                | Description                                                               |
| ---------------------- | ------------------------------------------------------------------------- |
| **Multiple selection** | Up to 10 molecules can be overlaid. Selecting more displays the first 10. |
| **Click molecule**     | Loads nearby pocket residues and highlights proposed interactions.        |
| **Download**           | Top-right button exports 3D structures of loaded molecules.               |

### Progressive Flow Chart

This 2D plot visualizes relative scores across various Boltz affinity metrics or RDKit descriptors within the screen.

<Frame>
  <img src="https://mintcdn.com/boltzpbc/vVhblbMfOGhVgP3r/images/user-guide/flow-chart.png?fit=max&auto=format&n=vVhblbMfOGhVgP3r&q=85&s=a1e0b98283a1da7ea92d1d45eaf152fb" alt="Progressive flow chart filtering" width="920" height="502" data-path="images/user-guide/flow-chart.png" />
</Frame>

Click and drag over a vertical column to apply filter ranges to the dataset. Highlighted lines show molecule trajectories through these filters. The table updates to show only molecules within the filtered ranges.

<Tip>
  Hover over a line to display the molecular structure and ID in the tooltip.
</Tip>

***

## Triage UI

The **Triage** UI allows collaborative or independent assessment of virtual screen output with a focused, structure-centric view for each molecule design.

<img src="https://mintcdn.com/boltzpbc/tEZyK9wozfHwPONX/images/image-28.png?fit=max&auto=format&n=tEZyK9wozfHwPONX&q=85&s=1f04bdad09b1f25b6d61085e91ac9377" alt="Image" width="1895" height="996" data-path="images/image-28.png" />

### Triage Actions

<CardGroup cols={2}>
  <Card title="Upvote" icon="thumbs-up">
    Mark molecules you favor based on available data
  </Card>

  <Card title="Downvote" icon="thumbs-down">
    Mark molecules you disfavor
  </Card>

  <Card title="Flag" icon="flag">
    Flexible marking for problematic predictions, chemical motifs, or molecules warranting discussion
  </Card>

  <Card title="Star" icon="star">
    Mark as 'active' to add to the Catalog
  </Card>
</CardGroup>

### Keyboard Shortcuts

| Action                   | Shortcut           |
| ------------------------ | ------------------ |
| Previous / Next Molecule | **← →** arrow keys |
| Upvote / Downvote + Flag | **3**              |
| Flag                     | **2**              |
| Downvote                 | **1**              |

### Tags

Tags allow free-form labelling shared across the Design Project. Multiple tags can be added to a molecule. When creating a new tag, a longer description can be provided while keeping the tag name short for a clean interface.

Select **Tags** from the left-hand menu to review all tags later.

***

## Catalog

The **Catalog** captures all 'active' molecules within a Design Project, forming a database across all Experiments and Virtual Screens.

<Frame>
  <img src="https://mintcdn.com/boltzpbc/vVhblbMfOGhVgP3r/images/user-guide/catalog.png?fit=max&auto=format&n=vVhblbMfOGhVgP3r&q=85&s=f43fd0b33c070fa28b8ffb981b5e87dd" alt="Design project catalog" width="1699" height="1012" data-path="images/user-guide/catalog.png" />
</Frame>

<Info>
  Active molecules in the Catalog are designs of particular interest to the Design Project team.
</Info>

The Catalog shares the same features as the Table UI. Unchecking the ⭐ sets a molecule back to inactive and removes it from the Catalog.

### Recommended Workflow

1. Collaboratively (or independently) upvote, downvote, or flag molecules in the Table or Triage UI from a Virtual Screen
2. After all users have made triage recommendations, mark selected molecules as 'active' to add them to the Catalog
3. Use the Catalog as a shortlist for design review meetings or further analysis