Skip to main content

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.

​
Overview

Virtual screens generate protein binder candidates using AI. You can pause and resume screens at any time.

​
Creating a New Virtual Screen

New protein design screen form
  1. From an experiment, click “New virtual screen” or “Virtual Screen”.
  2. Name - Enter a name for this protein design screen (e.g., “Small virtual screen to test the setup”)
  3. Type - Choose your screen type:
    Use AI to generate protein binders for your target. This is the most common option for discovering new candidates.
  4. Budget - Set the maximum number of protein designs to generate:
    Budget below 5k may not be sufficient to find good candidates. Start with a small pilot (50-100 designs) to validate your setup, then scale up to 10k-100k designs for production runs.
    • Use the slider to select: 10, 1k, 5k, 25k, 125k, or 625k
    • Estimated cost is displayed below
  5. Design Specification - Select a binder specification to use for generating protein designs
    • Shows binder specification details: Chains, Motifs, Designed residues
    • Only binder specifications added to your project are shown
  6. Target - Select the target to design binders against
    • Shows target details: number of chains and residues
    • Only initialized targets are available
  7. Experiment - Select an experiment for this virtual screen
    • Choose from existing experiments or create a new one
    • If no experiments exist, you’ll be prompted to create one
  8. Click “Start Protein Design” to begin.

​
Monitoring Virtual Screens

New protein design screen form
While a screen is running, you can:
  • View progress - See “Waiting for first candidates to be generated…” with elapsed time
  • Pause - Temporarily pause the screen
  • Stop Run - Cancel the screen entirely
  • View Results in Experiment - Navigate to see candidates as they’re generated

​
Status Indicators

  • RUNNING (blue) - Screen is actively generating candidates
  • COMPLETED (green) - Screen has finished generating all candidates
  • PAUSED - Screen is paused and can be resumed

​
Viewing Results

Virtual screen completed results
Once completed, the screen overview shows:

​
Performance Metrics

Top Performers: Binding Confidence
  • Tracks the best, 10th best, and 100th best candidates over time
  • Shows how binding confidence improves as more candidates are processed
Candidates Above Binding Confidence Thresholds
  • Cumulative count of candidates exceeding threshold values (>0.5, >0.6, >0.7, >0.8)
  • Helps assess overall screen quality

​
Screen Details

  • Status: COMPLETED
  • Total Generated: Number of candidates created
  • Added to experiment: Number automatically added (top performers)
  • Settings: Binder specification modality, chains, candidate budget
Click “View Results in Experiment” to see all candidates and begin triage.