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Protein Binder Design Tool Selection

Helps you choose between BoltzGen, BindCraft, RFdiffusion and Germinal, then lays out the full de novo binder design pipeline.

AutomationAdvanced★ 163⑂ 29AI score 6/10Last updated: Jul 1, 2026

What it does

  • Gives a decision tree for picking a binder design tool based on target type (standard protein, ligand binding, peptide/nanobody, diversity-driven exploration).
  • Compares BoltzGen, BindCraft, RFdiffusion and Germinal in a strengths/weaknesses table.
  • Provides a recommended pipeline (target prep → hotspot selection → BoltzGen → Chai validation → QC filtering) with a sample YAML config and modal run commands.
  • Supplies concrete filter thresholds (pLDDT > 0.80, ipTM > 0.50, PAE_interface < 10, scRMSD < 2.0 Å), per-stage design counts, and expected compute timelines.
  • Flags common mistakes such as buried hotspots, over-constraining, and sloppy target preparation.

Who it's for

  • Computational protein engineers and biologics discovery teams running de novo binder campaigns.
  • Teams on an RFdiffusion + ProteinMPNN workflow weighing a move to all-atom models like BoltzGen.
  • Anyone sizing and scheduling a GPU/Modal-based design campaign.

Example uses

  1. "Here's my PDB target, I want a 70–100 residue binder" → skill recommends BoltzGen and drafts binder.yaml with hotspot residues.
  2. "I need a VHH nanobody" → routes you to the Germinal skill instead.
  3. "How long to generate 500 backbones and validate them?" → uses the count and timeline tables to estimate 1–2 days of compute.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/BioTender-max/awesome-bio-agent-skills/HEAD/skills/adaptyv/binder-design/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/adaptyv/binder-design folder from the GitHub repo BioTender-max/awesome-bio-agent-skills into my ~/.claude/skills/binder-design/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/BioTender-max/awesome-bio-agent-skills.git && mkdir -p ~/.claude/skills && cp -r awesome-bio-agent-skills/skills/adaptyv/binder-design ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open your terminal.
  2. Clone the repo: git clone https://github.com/BioTender-max/awesome-bio-agent-skills.git
  3. Create the skills directory: mkdir -p ~/.claude/skills
  4. Copy the skill: cp -r awesome-bio-agent-skills/skills/adaptyv/binder-design ~/.claude/skills/
  5. Optionally copy the companion skills it references (boltzgen, rfdiffusion, bindcraft, germinal, protein-qc, pdb) the same way.
  6. Restart Claude Code and ask something like "help me choose a binder design tool for this target".
  7. For actual runs you'll separately need a Modal account, GPU access, and the modal_*.py runner scripts — set those up first.
View source on GitHub ↗License: NOASSERTION