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 zongtingwei/Bioclaw_Skills_Hub --skill binder-design-tool-selectiongit clone --depth 1 https://github.com/zongtingwei/Bioclaw_Skills_HubWrote 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/zongtingwei/bioclaw_skills_hub/binder-design-tool-selection)<a href="https://agentmods.dev/skills/zongtingwei/bioclaw_skills_hub/binder-design-tool-selection"><img src="https://agentmods.dev/badge/skills/zongtingwei/bioclaw_skills_hub/binder-design-tool-selection/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/zongtingwei/bioclaw_skills_hub/binder-design-tool-selection"><img src="https://agentmods.dev/badge/skills/zongtingwei/bioclaw_skills_hub/binder-design-tool-selection.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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 | $0.00091 | $0.01476 |
| Opus 5 | $0.00046 | $0.00738 |
| Sonnet 5 | $0.00018 | $0.00295 |
| Haiku 4.5 | $0.00009 | $0.00148 |
Grade A, and why
binder-design-tool-selection 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 13d 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 — 207 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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 ProteinMPNN | Exploration, diversity |
| Germinal | Nanobody/VHH design | Specialized | Antibody optimization |
Recommended Pipeline: BoltzGen → Chai → QC
BoltzGen provides all-atom design with built-in side-chain packing:
Target → BoltzGen → Validate → Filter
(pdb) (all-atom) (chai1-structure-prediction) (qc)
1. Target preparation
# Fetch structure from PDB
# Use pdb skill for guidance
- Trim to binding region + 10A buffer
- Remove waters and ligands
- Renumber chains if needed
2. Hotspot selection
- Choose 3-6 exposed residues
- Prefer charged/aromatic residues
- Cluster spatially (within 10-15A)
3. Design with BoltzGen (Recommended)
First, create a YAML config file (e.g., binder.yaml):
entities:
- protein:
id: B
sequence: 70..100
- file:
path: target.cif
include:
- chain:
id: A
binding_types:
- chain:
id: A
binding: 45,67,89
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.
- 13d ago First seen · 207 lines · 91 tokens per session scan A c11ae8f15623
binder-design-tool-selection is a skill published in the GitHub repository zongtingwei/Bioclaw_Skills_Hub (26 stars, last pushed 5mo ago), licensed MIT. It adds 91 tokens to every session and 1,476 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
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…
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
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
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…
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…