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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.

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Overview

Binder specifications define the protein binder properties (modality, structure, design regions) that will be used to generate candidates.

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Creating a New Binder Specification

Nanobody specification structure selection
  1. From your project dashboard, click ”+ Add” in the Binder Specifications section.
  2. Step 1: Setup - Give your binder specification a name and choose the protein modality:

    Peptide

    Design short peptide sequences

    Antibody

    Create antibody heavy and light chains

    Nanobody

    Design single-domain antibodies

    Other

    Other protein types
  3. Click ”> Continue to Specification”.

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Starting Specification

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Option 1: Structure-Based Specification

Nanobody specification structure selection
Select a template:
  • Choose from pre-loaded structures (e.g., vWF A1-Caplacizumab Complex, IL-6R-Vobarilizumab Complex)
  • Each template shows PDB ID and description
Or import your own:
  • Enter a PDB ID and Assembly ID (default: 1), then click “Import”
  • Or upload a structure file (.cif, .cif.gz, etc.)

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Option 2: Sequence-Based Specification

Click the “Sequence” tab to add sequences directly instead of using a structure.

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Select Residues

Select residues for nanobody specification
Select the residues you want to include in your design:
  • Recommended: ≤300 residues
  • Use CDR1, CDR2, CDR3 quick-select buttons for antibodies/nanobodies
  • Or manually select by clicking and dragging on the sequence
  • Selected residues are highlighted in green
  • The 3D structure updates to show selected regions
Numbering schemes:
  • Chothia (default) or Kabat numbering for antibodies/nanobodies
  • Switch between schemes using the tabs above the sequence
Click ”> Continue to Design” when done.

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Design Configuration

Configure design motifs and constraints:
Nanobody specification structure selection

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Excluded Amino Acids

Specify amino acids that will not be used in designed regions (e.g., exclude Cysteine to prevent unwanted disulfide bonds).
Nanobody specification structure selection

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Create Design Motifs

  1. Select residues on the sequence or 3D structure
  2. Right-click or use the context menu to “Replace with design motif”
  3. For CDR regions, you can specify:
    • Fixed length - Replace with same number of residues
    • Variable length - Specify a range (e.g., 10-25 residues for CDR3)
Nanobody specification structure selection
Nanobody specification structure selection
Nanobody specification structure selection

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Motif Management

  • Each motif is color-coded and shown in the sequence viewer
  • Click a motif to edit it
  • Click the X on a motif to remove it
  • Summary shows total residues and number of motifs
Click ”> Create Specification” when ready.

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After Binder Specification Creation

Once your binder specification is created, you’ll see options to:
  • Generate binders with AI - Start a virtual screen using this binder specification
  • Create Another Target - Add another target to design binders against
  • Skip for now - Continue later