> ## 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.

# Virtual Screening - Setup

> Run generative designs or screen custom libraries

Once a Target is created, Boltz Lab witll guide you through starting your first **Virtual Screen**

<img src="https://mintcdn.com/boltzpbc/01Dj948NLM75wx38/images/image-21.png?fit=max&auto=format&n=01Dj948NLM75wx38&q=85&s=0d4386ab7334bb13a97f705653ba9a35" alt="Image" width="960" height="563" data-path="images/image-21.png" />

## Creating an Experiment

Follow the instruction and select  **+** **Create New Experiment** fromprompts

<img src="https://mintcdn.com/boltzpbc/01Dj948NLM75wx38/images/image-22.png?fit=max&auto=format&n=01Dj948NLM75wx38&q=85&s=1936254c50fa38ce4de50c56cf131a58" alt="Image" className="mx-auto" style={{ width:"89%" }} width="763" height="448" data-path="images/image-22.png" />

Give the **Experiment** a name and a hypothesis that describes the work being carried out. The Experiment space is collaborative and accessible to other users within the organization.

<Tabs>
  <Tab title="❌ Poor Example">
    **Name:** Experiment 1

    **Hypothesis:** Molecules for screening
  </Tab>

  <Tab title="✅ Good Example">
    **Name:** WT Kinase Series 1

    **Hypothesis:** Exploring H-bond donors at R2 position of series core to improve kinase binding affinity to wild-type Kinase A, while maintaining solubility. Enumerated library from Supplier building-block library.
  </Tab>
</Tabs>

To continue, click **New Virtual Screen**.

***

## Generative Virtual Screen

A **Generative** screen uses generative AI models and active learning to search molecular space and find binders for the selected Target, optimizing the predicted binding confidence.

<img src="https://mintcdn.com/boltzpbc/01Dj948NLM75wx38/images/download(1).png?fit=max&auto=format&n=01Dj948NLM75wx38&q=85&s=0b0cb58ddcc8944cc9d508b57a333034" alt="Download (1)" width="1037" height="953" data-path="images/download(1).png" />

### Parameters

<AccordionGroup>
  <Accordion title="Target Selection">
    If multiple Targets are added to the Design Project, select the target you want to optimize affinity for.
  </Accordion>

  <Accordion title="Chemical Space">
    By default, a generative screen searches within the expanded \~75B Enamine REAL Space. This ensures all output molecules are theoretically synthesizable. Alternatively, choose not to apply any chemical-space filter.
  </Accordion>

  <Accordion title="Molecule Structure Filtering">
    **Normal Filtering** (default): Curated filtering excluding most problematic molecules but allowing some motifs (phenols, anilines, aryl halides, esters) that can be optimized away in later design cycles.

    **Extra Filtering**: Extends to include functional groups with chemical stability issues.

    **Aggressive Filtering**: Applies aggressive filtering to remove edge cases.
  </Accordion>

  <Accordion title="Molecule Filters">
    Specify filters based on RDKit molecular descriptors to keep small-molecule generation within your desired molecular/physicochemical space. **Preset** filters are available for convenience.

    <Tip>
      Set filters at generation time rather than filtering afterwards to optimize compute usage.
    </Tip>
  </Accordion>

  <Accordion title="Budget">
    Sets the maximum number of molecules for generation and scoring. You can pause/stop the screen at any time.

    <Warning>
      It is recommended **not** to run fewer than 20,000 molecules, as this typically does not allow convergence in the active learning model.
    </Warning>
  </Accordion>
</AccordionGroup>

***

## Library Virtual Screen

**Custom** or **Pre-computed Libraries** can alternatively be screened by selecting **Library (CSV)**.

### Upload CSV

The file should contain a **SMILES** column with the molecules identifier.

<Frame>
  <img src="https://mintcdn.com/boltzpbc/vVhblbMfOGhVgP3r/images/user-guide/library-upload.png?fit=max&auto=format&n=vVhblbMfOGhVgP3r&q=85&s=ba55658401b2c290eef7803078d90b14" alt="CSV upload interface" width="1038" height="403" data-path="images/user-guide/library-upload.png" />
</Frame>

### Pre-computed Libraries

Pre-computed vendor compound libraries can be selected without needing to upload CSV files.

<Frame>
  <img src="https://mintcdn.com/boltzpbc/vVhblbMfOGhVgP3r/images/user-guide/precomputed-libraries.png?fit=max&auto=format&n=vVhblbMfOGhVgP3r&q=85&s=f14fca3232d4b652832a874195f24c95" alt="Pre-computed library selection" width="1037" height="385" data-path="images/user-guide/precomputed-libraries.png" />
</Frame>

<Tip>
  **Cross-screening tip:** For screening molecules against multiple targets, export the desired molecule designs from your Experiment or Virtual Screen, and use them as a custom library in the same or new Experiment for cross-target/off-target Boltz predictions.
</Tip>
