Binder design · Protein Design

BindCraft

Design de novo protein or peptide binders against a target structure.

Builds a BindCraft target/advanced/filter settings trio and runs the official pipeline end to end (hallucination, ProteinMPNN redesign, AlphaFold2 validation, and filtering).

Documentation ↗ Source code ↗

Input

Configure a small job

POST

Binder name

Target PDB

Target chain IDs Comma-separated chain IDs.

Hotspot residues (optional) One "chain: residues" per line, e.g. "A: 54,56,58" or "A: 1-10". Leave blank to let AF2 pick a binding site.

Minimum binder length BindCraft's own default range is 65-150 for protein binders, 10-20 for peptides.

Maximum binder length

Accepted designs requested

Filter set

Omit amino acids One-letter amino-acid codes ProteinMPNN redesign must not sample.

Use BigBang initialization

Helicity weight Negative biases toward helical binders, positive toward non-helical, 0 is neutral.

Bias toward beta-sheet designs

Use ProteinMPNN-biased trajectory design

Allow a flexible target interface

Treat the target as a hard (rigid) target

Average pLDDT threshold

Average pTM threshold

Average interface pTM threshold

Average interface PAE threshold

Average surface hydrophobicity threshold

Minimum interface residues

Minimum interface H-bonds

Maximum hotspot RMSD, angstrom

Average binder pLDDT threshold

Maximum binder RMSD, angstrom

Maximum run time, minutes Bounds this request's own subprocess; BindCraft itself has no built-in time limit.

Ready

Response

JSON result

{
  "status": "Ready for a request"
}