rfd4-proteina-search SKILL.md skillA
rfd4-proteina-search 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/rfd4-proteina-search@git:20261020.65f97c4Pins git:20261020.65f97c4 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/rfd4-proteina-search/SKILL.md- Versions recorded
- 1
- Latest version
- git:20261020.65f97c4, committed Oct 20, 2026
- Size
- 12,611 bytes
- Repository stars
- 503
- License
- a license file GitHub does not identify
Use when running RFD4-Proteina reward-guided beam search with chosen checkpoints, branching, metrics, and compute limits.
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
# RFD4-Proteína Reward-Guided Search ## Purpose ## Reward requirements Complete `rfd4-proteina-setup` first. Generation requires a CUDA GPU. Rewards listing refolding oracles also require a configured refolding backend; RFD4-Proteína supports AF2, AF3, and OpenFold3 through `metrics/refolding_oracles`. Rewards such as `interchain_interactions` do not require a refolding oracle. Search explores multiple generation trajectories and keeps the candidates a **reward** scores highest. **Beam search** ships ready to run: it branches and prunes partial trajectories at step checkpoints, scoring survivors with a reward model. The shipped `inference_beam_example` uses the default **AF3 oracle** for refolding confidence; other search configs may select another backend or avoid refolding entirely. Search runs through the **same entry point as generation** — `generate.py` — selected by an `inference_experiment` config that adds one `search:` block. All arguments are Hydra `key=value` (never `--key value`). Run everything from the repository root (the directory containing `.project-root`). ## Prerequisites …
Read the whole file at its exact version.
How to install
mdr add nvidia-bionemo/bionemo-agent-toolkit/rfd4-proteina-search@sha256:44bbc87391b41291The line at the top of this page pins the label git:20261020.65f97c4, 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_b3bz7xlkoyzeomxu)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Oct 20, 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 (12611 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_b3bz7xlkoyzeomxu GET https://markdownregistry.com/api/v1/resolve?ref=nvidia-bionemo/bionemo-agent-toolkit/rfd4-proteina-search GET https://markdownregistry.com/api/v1/blob/44bbc87391b41291dc1f1a93e750d5d1f51e2ec64172b5985ac22aeb0b2aba45
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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