Results and Triage

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Overview

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Experiment View

• Overview - Summary statistics and metrics
• Table - List view of all candidates with filters and sorting
• Triage - Organized view for candidate evaluation

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Candidate Table

• Sequence - Protein sequence with CDR regions highlighted (for antibodies/nanobodies)
• Id - Unique identifier (e.g., NB-X7CMZA38)
• Triage - Thumbs down, flag, and thumbs up counts
• Created By - Which virtual screen generated this candidate
• Created - Timestamp when the candidate was generated
• Binding Confidence - Predicted binding affinity score for the target
• Structure Confidence - Overall structure quality score

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Filtering and Selection

• Default view dropdown - Pre-configured filter sets
• Columns button - Show/hide table columns
• Filters button - Add custom filters including:
  • Text filters - Filter by Id, Created By, etc.
  • Number filters - Filter by ipTM, pLDDT, Binding Confidence, Structure Confidence, Loop Fraction using sliders
  • Filter chips show active filters and can be removed individually
• Select candidates - Use checkboxes to select multiple candidates
• Download - Export selected candidates

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Bulk Actions

• Add to experiment - Move to another experiment
• Tag - Apply tags for organization
• Download - Export candidate data

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3D Visualization

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Target Selection

• Dropdown to switch between targets
• Selected candidate IDs displayed as colored tags
• Download and fullscreen options

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3D Structure Viewer

• Interactive 3D ribbon diagram showing:
  • Target (light grey)
  • Binder candidates (colored by selection)
• 3D axis indicator for orientation
• Rotate, zoom, and pan controls

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Properties Comparison

• ipTM - Interface predicted Template Modeling score
• pLDDT - Predicted Local Distance Difference Test (structure confidence)
• Binding Confidence - Predicted binding affinity
• Structure Confidence - Overall structure quality

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Triage View

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Left Panel - Candidate Details

• Sequence Viewer:
  • Full protein sequence with Framework Regions (FR) and Complementarity Determining Regions (CDR) highlighted
  • CDR regions color-coded (CDR1, CDR2, CDR3)
  • Residue numbers displayed above sequence
  • Navigation arrows to move between candidates
• Candidate Actions:
  • Star - Favorite a candidate
  • Thumbs down - Reject candidate
  • Flag - Mark for further review
  • Thumbs up - Approve candidate
  • + Tag - Apply tags for organization
• Properties and Descriptors:
  • Properties tab - View metrics (ipTM, pLDDT, Binding Confidence, Structure Confidence)
  • Descriptors tab - View structural features (Loop Fraction, Helix Fraction, Sheet Fraction)
  • Switch between Table and Plot views for each

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Right Panel - 3D Structure and Comparison

• 3D Structure Viewer:
  • Shows the selected candidate’s binding pose with the target
  • Binder colored orange, target colored light grey/green
  • Interactive controls for rotation, zoom, and pan
• Properties Comparison:
  • Parallel coordinates plot showing all candidates
  • Selected candidate highlighted in purple
  • Non-selected candidates shown in dark grey
  • Compare across multiple properties simultaneously

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Triage Workflow

1. Select candidates - Use checkboxes or filters to narrow down
2. Review 3D structures - Examine binding poses in the viewer
3. Compare properties - Use charts to identify high-scoring candidates
4. Triage actions:
   • Thumbs down - Reject candidate
   • Flag - Mark for further review
   • Thumbs up - Approve candidate
5. Tag candidates - Apply tags for organization (e.g., “high-affinity”, “interesting-pose”)
6. Export - Download selected candidates for further analysis

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Tips

• Start by filtering to top performers (high binding confidence)
• Review 3D structures to ensure poses are reasonable
• Compare multiple candidates side-by-side using the properties charts
• Use tags to organize candidates by different criteria
• Export promising candidates for experimental validation