Getting it into your agent
It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.
git clone --depth 1 https://github.com/adaptyvbio/protein-design-skillsnpx agentmods add skills/adaptyvbio/protein-design-skills/bindcraftWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/adaptyvbio/protein-design-skills/bindcraft)<a href="https://agentmods.dev/skills/adaptyvbio/protein-design-skills/bindcraft"><img src="https://agentmods.dev/badge/skills/adaptyvbio/protein-design-skills/bindcraft/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/adaptyvbio/protein-design-skills/bindcraft"><img src="https://agentmods.dev/badge/skills/adaptyvbio/protein-design-skills/bindcraft.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00104 | $0.01561 |
| Opus 5 | $0.00052 | $0.00781 |
| Sonnet 5 | $0.00021 | $0.00312 |
| Haiku 4.5 | $0.00010 | $0.00156 |
Grade A, and why
bindcraft scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 195 lines — stays where its author put it; the contents beside it link to each section on GitHub.
BindCraft Binder Design
Prerequisites
| Requirement | Minimum | Recommended |
|---|---|---|
| Python | 3.9+ | 3.10 |
| CUDA | 11.7+ | 12.0+ |
| GPU VRAM | 32GB | 48GB (L40S) |
| RAM | 32GB | 64GB |
How to run
First time? See Getting started to set up Modal and biomodals.
Option 1: Modal (recommended)
cd biomodals
modal run modal_bindcraft.py \
--input-pdb target.pdb \
--target-chains A \
--target-hotspot-residues "45,67,89" \
--lengths "70,100" \
--number-of-final-designs 50
GPU: L40S (48GB) | Timeout: 300 min default
Option 2: Local installation
git clone https://github.com/martinpacesa/BindCraft.git
cd BindCraft
# BindCraft is configured with JSON files, not flags
python -u ./bindcraft.py \
--settings ./settings_target/mytarget.json \
--filters ./settings_filters/default_filters.json \
--advanced ./settings_advanced/default_4stage_multimer.json
The target PDB, chains, hotspots, and binder length range are set inside the
--settings JSON. See the BindCraft repo for the settings schema.
Key parameters (Modal wrapper)
| Parameter | Default | Description |
|---|---|---|
--input-pdb |
required | Target structure |
--target-chains |
A |
Target chain(s) |
--target-hotspot-residues |
"" | Target hotspots (e.g. "45,67,89") |
--lengths |
50,130 |
Binder length range |
--number-of-final-designs |
1 | Passing designs to return |
--max-trajectories |
none | Cap on trajectories |
Output format
output/
├── design_0/
│ ├── binder.pdb # Final design
│ ├── complex.pdb # Binder + target
│ ├── metrics.json # QC scores
│ └── trajectory/ # Optimization trajectory
├── design_1/
│ └── ...
└── summary.csv # All metrics
Metrics Output
{
"plddt": 0.89,
"ptm": 0.78,
"iptm": 0.62,
"pae": 8.5,
"rmsd": 1.2,
"sequence": "MKTAYIAK..."
}
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 195 lines · 104 tokens per session scan A 5816d52cd405
bindcraft is a skill published in the GitHub repository adaptyvbio/protein-design-skills (158 stars, last pushed 2mo ago), licensed MIT. It adds 104 tokens to every session and 1,561 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
Other skills, from other repositories
bindcraft
End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high…
bindcraft
End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high…
bindcraft
End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high…
bindcraft
End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high…
protein-structure-design-boltzgen
All-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from the start, (2) Designing around small molecules or ligands, (3) Want all-atom diffusion (not just backbone), (4) Require precise binding geometries, (5) Using YAML-based configuration. For structure…
boltzgen
All-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from the start, (2) Designing around small molecules or ligands, (3) Want all-atom diffusion (not just backbone), (4) Require precise binding geometries, (5) Using YAML-based configuration. For backbone-only…