protein-binder-design SKILL.md skillA
This file is byte-identical to the first copy the registry indexed. Same content hash, so the same checks give both the same grade.
protein-binder-design from nvidia-bionemo/bionemo-agent-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add nvidia-bionemo/bionemo-agent-toolkit/protein-binder-design@git:20260825.0e67a61Pins git:20260825.0e67a61 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- nvidia-bionemo/bionemo-agent-toolkit
- Path
skills/bionemo-agent-toolkit/skills/protein-binder-design/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260825.0e67a61, committed Aug 25, 2026
- Size
- 5,795 bytes
- Repository stars
- 503
- License
- a license file GitHub does not identify
Orchestrate an end-to-end de novo protein binder design campaign against a protein target by composing BioNeMo NIM skills. Use for binder design, minibinder design, de novo binders, RFdiffusion + ProteinMPNN + Boltz2/OpenFold3 pipelines, epitope/hotspot-targeted design, in-silico binder validation, and ranking designs by interface confidence.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Protein Binder Design (workflow) Run a de novo binder design campaign by composing atomic NIM skills. This skill owns orchestration, handoff contracts, filtering, validation, and the run manifest. It does NOT duplicate per-NIM API details — defer those to each atomic skill's `SKILL.md`. ## Composed skills | Step | Skill | Owns | |---|---|---| | Backbones | `rfdiffusion-nim` | binder backbone PDBs (contigs + hotspots) | | Sequences | `proteinmpnn-nim` | sequences for each backbone | | Co-fold / score | `boltz2-nim` or `openfold3-nim` | binder–target complex + confidence / ipTM | | MSA (optional) | `msa-search-nim` | target A3M for higher-quality folding | The atomic NIM skills are recommended companions (one per NIM, from the BioNeMo NIM skill set). They are **not required**: `references/pipeline.md` carries the concrete request shape for every NIM call, so an agent with NIM access can follow this skill standalone. For endpoints/auth see **Configuration** below. ## Pipeline 1. **Target prep** — get the target PDB + epitope; map epitope/hotspot author residue numbers to RFdiffusion `hotspot_res` strings; optionally build a target MSA with `msa-search-nim`. …
Read the whole file at its exact version.
How to install
mdr add nvidia-bionemo/bionemo-agent-toolkit/protein-binder-design@sha256:a9bfe2b3a477fd1bThe line at the top of this page pins the label git:20260825.0e67a61, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_xf6v4hgivzhyban7)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Aug 25, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (5795 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
nvidia-bionemo/bionemo-agent-toolkit · 503 stars · license a license file GitHub does not identify · pushed 2026-11-05 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_xf6v4hgivzhyban7 GET https://markdownregistry.com/api/v1/resolve?ref=nvidia-bionemo/bionemo-agent-toolkit/protein-binder-design GET https://markdownregistry.com/api/v1/blob/a9bfe2b3a477fd1bc95efca8617e015f7202e9e00d902b4549d5985b258f9fa1
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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