Use BoltzGen

Official Neurosnap webserver for accessing BoltzGen online.

BETA Protein Design Developability Proteins

Overview

BoltzGen is a universal all-atom generative model for biomolecular binder design. It unifies sequence design and structure prediction within a single diffusion-based framework, enabling the creation of high-affinity binders against proteins, nucleic acids, and small molecules. Through a geometry-based representation and a flexible design specification language, BoltzGen allows precise control over covalent bonds, structural motifs, and binding interfaces while maintaining state-of-the-art folding accuracy.

Neurosnap Overview

The BoltzGen online webserver allows anybody with a Neurosnap account to run and access BoltzGen, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong terms of service and privacy policy.

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Features

  • Unifies structure prediction and binder design in a single all-atom diffusion framework.
  • Supports protein, peptide, nanobody, and cyclic peptide binders targeting proteins, nucleic acids, or small molecules.
  • Enables controllable generation of diverse and designable binders through architecture-level conditioning and tunable noise schedules.
  • Includes a downstream pipeline for inverse folding, affinity estimation, and physics-based filtering to identify top candidates for experimental validation.
  • Validated experimentally across 26 targets, achieving nanomolar-affinity binders in most tested protein and peptide campaigns.

Statistics

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API Request

Access BoltzGen using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.

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Job Note

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Configuration & Options

Important Information

BoltzGen supports multiple binder design protocols. Protein, Peptide, and Nanobody modes require a template structure for the target chains, while the Protein-Small Molecule mode expects a ligand definition (SMILES string, CCD code, or SDF file).

Mode Selection

Choose which BoltzGen workflow to run. Structure-based modes (Protein, Peptide, Nanobody) design binders against a target protein. Protein-Small Molecule creates binders around a ligand definition.

Shared Parameters

Smallest amino acid length allowed for generated binders.

Largest amino acid length allowed for generated binders.

Number of intermediate designs to sample across all batches before diversity optimization.

Number of diffusion samples to generate per trunk run. If not specified, this defaults to 1 if the number of designs is less than 100, and 10 otherwise. Note that for design tasks that randomly sample the binder length (or use randomness in other ways), all designs generated in the same batch will share the same length. Having a large diffusion batch size compared to the total number of designs to generate will therefore not evenly sample the possible lengths.

Size of the final diversity-optimized set.

Enable to request cyclic binders. Applies to Peptide mode.

Protein / Peptide / Nanobody Inputs

Reference protein structure containing the target chains to bind against. Provide a single model containing the chains referenced below.

Comma-separated list of chain identifiers (e.g., "A,B") from the target structure to include in the binding interface.

Protein-Small Molecule Inputs

Ligand definition for the Protein-Small Molecule mode. Supply an SDF file, a SMILES string, or specify a CCD code to seed binder generation around the small molecule.

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