Run BindCraft online

Pick BindCraft when you have a target PDB plus known hotspot residues and want de novo 60-150 aa protein binders.

BindCraft (Pacesa et al., bioRxiv 2024). De novo binder design via AlphaFold2-Multimer hallucination with hotspot-focused backpropagation, followed by ProteinMPNN sequence design and AF2 re-prediction filtering.

When it fits:

• You have a target PDB and at least one hotspot residue you want the binder to contact.
• You want de novo 50–150 aa protein binders (not antibodies).
• You can wait ~45 min per pilot run and want filtered hits with ipTM and pLDDT above the BindCraft default thresholds.

Use the score legend below to read results. Each tool reports a subset of these depending on whether it does design, sequence recovery, or structure prediction.

ipTM

Predicted confidence in the binder to target interface. Higher is better. Aim above roughly 0.7 on a tractable target.

pLDDT

Per-residue confidence in the predicted fold. Higher means the model is more sure of that part of the structure.

i_pAE and pAE

Predicted alignment error, at the interface (i_pAE) or across the whole structure (pAE). Lower is better.

ProteinMPNN recovery

Fraction of native residues recovered when ProteinMPNN redesigns a known sequence on its native backbone. Higher is better; well calibrated above roughly 0.4 on diverse folds.

45 min per run on a dedicated GPU. Billing is by the second of compute, so a faster preset costs less.

We keep a plain-English overview of BindCraft on the main Ranomics site — what the model does under the hood, the kinds of targets it works on, and where it fits inside a full design-to-wet-lab campaign.

If you are picking between BindCraft and a sibling algorithm, these run on the same hub against the same target.

Run RFdiffusion online

Pick RFdiffusion when you want general de novo binder design scored by AF2 multimer (ipTM / pLDDT / i_pAE). For antibody and nanobody scaffolds use RFantibody, for AF2-IG initial-guess scoring use PXDesign, and for hallucination-driven binders without AF2 filtering use BindCraft.

Run BoltzGen online

Pick BoltzGen when you want one model that can design mini-proteins, nanobodies, antibodies, or peptides against the same target, or when your target involves glycans, post-translational modifications, or non-canonical residues.

Run PXDesign online

Pick PXDesign when AF2 confidence against a defined target matters and you want real ipTM / pLDDT / pAE on every candidate. For hallucination-driven binder design without AF2 filtering use BindCraft, for antibody and nanobody CDRs use RFantibody, and for target structure generation without binder design use BoltzGen.

Can I run BindCraft online without installing it?

Yes. Ranomics Tools runs the full BindCraft hallucination loop on a dedicated GPU through your browser. Upload a target PDB, pick hotspots and binder length, and candidates come back with AF2 ipTM and pLDDT on every hit.

BindCraft vs RFdiffusion — which should I pick?

Both design de novo binders against your target. BindCraft hallucinates sequences and backbones jointly inside AF2; RFdiffusion samples a backbone first then drops sequences in with ProteinMPNN. Run both on the same hub and compare ipTM before committing to wet-lab.

How long does a BindCraft pilot take?

Typical pilot runs finish in roughly 20 to 60 minutes on a dedicated A100, depending on target size and how many candidates pass the internal ipTM filter. Billing is by the second so a faster preset costs less.

Pacesa et al., bioRxiv 2024