Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add adaptyvbio/protein-design-skills --skill protein-design-workflowgit clone --depth 1 https://github.com/adaptyvbio/protein-design-skillsWrote 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/protein-design-workflow)<a href="https://agentmods.dev/skills/adaptyvbio/protein-design-skills/protein-design-workflow"><img src="https://agentmods.dev/badge/skills/adaptyvbio/protein-design-skills/protein-design-workflow/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/protein-design-workflow"><img src="https://agentmods.dev/badge/skills/adaptyvbio/protein-design-skills/protein-design-workflow.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 | $0.00083 | $0.01335 |
| Opus 5 | $0.00042 | $0.00668 |
| Sonnet 5 | $0.00017 | $0.00267 |
| Haiku 4.5 | $0.00008 | $0.00134 |
Grade A, and why
protein-design-workflow scanned grade A with 1 finding 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 12d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
curl -o target.pdb "https://files.rcsb.org/download/XXXX.pdb" How it starts
The opening of the file, as written. The whole thing — 200 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Protein Design Workflow Guide
Standard binder design pipeline
Overview
Target Preparation --> Backbone Generation --> Sequence Design
| | |
v v v
(pdb skill) (rfdiffusion) (proteinmpnn)
| |
v v
Structure Validation --> Filtering
| |
v v
(alphafold/chai) (protein-qc)
Phase 1: Target preparation
1.1 Obtain target structure
# Download from PDB
curl -o target.pdb "https://files.rcsb.org/download/XXXX.pdb"
1.2 Clean and prepare
# Extract target chain
# Remove waters, ligands if needed
# Trim to binding region + 10A buffer
1.3 Select hotspots
- Choose 3-6 exposed residues
- Prefer charged/aromatic (K, R, E, D, W, Y, F)
- Check surface accessibility
- Verify residue numbering
Output: target_prepared.pdb, hotspot list
Phase 2: Backbone generation
Option A: RFdiffusion (diverse exploration)
# RFdiffusion runs from the official repo, not biomodals
python run_inference.py \
inference.input_pdb=target_prepared.pdb \
contigmap.contigs=[A1-150/0 70-100] \
ppi.hotspot_res=[A45,A67,A89] \
inference.num_designs=500
Option B: BindCraft (end-to-end)
modal run modal_bindcraft.py \
--input-pdb target_prepared.pdb \
--target-hotspot-residues "45,67,89" \
--number-of-final-designs 100
Output: 100-500 backbone PDBs
Phase 3: Sequence design
For RFdiffusion backbones
for backbone in backbones/*.pdb; do
modal run modal_ligandmpnn.py \
--input-pdb "$backbone" \
--params-str "--number_of_batches 8 --temperature 0.1"
done
Output: 8 sequences per backbone (800-4000 total)
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.
- 12d ago First seen · 200 lines · 83 tokens per session scan A 3c89c63821f1
protein-design-workflow is a skill published in the GitHub repository adaptyvbio/protein-design-skills (159 stars, last pushed 3mo ago), licensed MIT. It adds 83 tokens to every session and 1,335 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
Other skills, from other repositories
end-to-end-protein-design-workflow
End-to-end protein design pipeline guide across preparation, generation, validation, and filtering. Use this skill when: (1) Starting a new protein design project, (2) Need step-by-step workflow guidance, (3) Understanding the full design pipeline, (4) Planning compute resources and timelines, (5) Integrating multiple…
end-to-end-protein-design-workflow
End-to-end protein design pipeline guide across preparation, generation, validation, and filtering. Use this skill when: (1) Starting a new protein design project, (2) Need step-by-step workflow guidance, (3) Understanding the full design pipeline, (4) Planning compute resources and timelines, (5) Integrating multiple…
protein-design-workflow
End-to-end guidance for protein design pipelines. Use this skill when: (1) Starting a new protein design project, (2) Need step-by-step workflow guidance, (3) Understanding the full design pipeline, (4) Planning compute resources and timelines, (5) Integrating multiple design tools. For tool selection, use…
protein-design-workflow
End-to-end guidance for protein design pipelines. Use this skill when: (1) Starting a new protein design project, (2) Need step-by-step workflow guidance, (3) Understanding the full design pipeline, (4) Planning compute resources and timelines, (5) Integrating multiple design tools.
binder-design
Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use…
binder-design-tool-selection
Binder design tool selection and workflow routing guidance. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use…