BindCraft API

The BindCraft API provides an interface to the BindCraft protein binder design tool. This tool takes as input a target PDB file and generates new novel protein binder PDBs with SolubleMPNN sequences by iteratively predicting and backpropagating through AlphaFold2.

Command Line Interface

Examples

Generate 100 binders for an input PDB with selected hotspots

lev engine submit bindcraft input.pdb \
  --chains A,B \
  --target-hotspots A23,A45,B12 \
  --min-length 5 \
  --max-length 15 \
  --num-models 100

Flags

  • --advanced-settings (str) (Optional)
    • Advanced settings in JSON format
  • --chains (str) (Required)
    • Chains to design (comma-separated)
    • Example:
      • "A,B"
  • --custom-filters (str) (Optional)
    • Custom filters for design
  • --gpu-type (str)
    • Select the GPU type to use.
    • Options:
      • t4 (default)
      • l4
      • a100
  • --max-length (int) (Default: 15)
    • Maximum peptide length
  • --min-length (int) (Default: 5)
    • Minimum peptide length
  • --num-models (int) (Default: 100)
    • Number of models to generate
  • --pdb-file (str) (Required)
    • The path to a PDB file containing the target you want to design binders for

      [!NOTE] You can specify this flag as the first positional argument or with the --pdb-file flag

  • --target-hotspots (str) (Optional)
    • Target hotspot residues
    • Example:
      • "A23,A45,B12"

Python Interface

Examples

Generate 100 binders for an input PDB with selected hotspots

from engine import EngineClient

client = EngineClient()
client.authorize()

job_id = client.submit_bindcraft(
    pdb_path="input.pdb",
    chains="A,B",
    target_hotspots="A23,A45,B12",
    min_length=5,
    max_length=15,
    num_models=100
)

Flags

  • advanced_settings (str) (Optional)
    • Advanced settings in JSON format
  • chains (str) (Required)
    • Chains to design (comma-separated)
    • Example:
      • "A,B"
  • custom_filters (str) (Optional)
    • Custom filters for design
  • gpu_type (str) (Optional)
    • Select the GPU type to use.
    • Options:
      • t4 (default)
      • l4
      • a100
  • max_length (int) (Default: 15)
    • Maximum peptide length
  • min_length (int) (Default: 5)
    • Minimum peptide length
  • num_models (int) (Default: 100)
    • Number of models to generate
  • pdb_path (str) (Required)
    • The path to a PDB file containing the target you want to design binders for
  • target_hotspots (str) (Optional)
    • Target hotspot residues
    • Example:
      • "A23,A45,B12"

Outputs

  • binders directory
    • A directory containing filter-passing binder designs from BindCraft.
  • run directories
    • N directories containing trajectory-specific data for each run requested with --num-models. Contains the filter values for accepted designs in final_design_stats.csv and final design filter plots in Accepted/Plots.

Updated: