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 the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).
npx skills add BioTender-max/awesome-bio-agent-skills --skill binder-design-tool-selection --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Binder Design Tool Selection **Plain-language role**: Use this skill to choose the right binder-design-tool-selection method, not to run the design model itself. ## Decision tree ``` De novo binder design? │ ├─ Standard target → BoltzGen (recommended) │ All-atom output (no separate ProteinMPNN step needed) │ Better for ligand/small molecule binding │ Single-step design (backbone + sequence + side chains) │ ├─ Need diversity/exploration → RFdiffusion + ProteinMPNN │ Maximum backbone diversity │ Two-step: backbone then sequence │ ├─ Integrated validation → BindCraft │ Built-in AF2 validation │ End-to-end pipeline │ ├─ Ligand binding → BoltzGen ✓ │ All-atom diffusion handles ligand context │ ├─ Peptide/nanobody → Germinal │ VHH/nanobody design │ Germline-aware optimization │ └─ Antibody/Nanobody +-- VHH design --> germinal skill ``` ## Tool comparison | Tool | Strengths | Weaknesses | Best For | |------|-----------|------------|----------| | BoltzGen | All-atom, single-step, ligand-aware | Higher GPU requirement | Standard (recommended) | | BindCraft | End-to-end, built-in AF2 validation | Less diverse | Production campaigns | | RFdiffusion | High diversity, fast | Requires ProteinM
- Decision tree
- Tool comparison
- Recommended Pipeline: BoltzGen → Chai → QC
- 1. Target preparation
- 2. Hotspot selection
- 3. Design with BoltzGen (Recommended)
- 4. Alternative: RFdiffusion Pipeline
- 5. Validation
- 6. Filtering
- Number of designs
- Common mistakes
- Wrong hotspots
- Insufficient diversity
- Poor target preparation
Fetch structure from PDB Use pdb skill for guidance modal run modal_boltzgen.py \ Step 1: Backbone generation modal run modal_rfdiffusion.py \ Step 2: Sequence design modal run modal_ligandmpnn.py \ modal run modal_chai1.py \
What does the binder-design-tool-selection skill do?
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 the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill binder-design-tool-selection --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.