complexa-design SKILL.md skillA
complexa-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/complexa-design@git:20261016.a6eced5Pins git:20261016.a6eced5 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
open-models-skills/proteina-complexa/complexa-design/SKILL.md- Versions recorded
- 3
- Latest version
- git:20261016.a6eced5, committed Oct 16, 2026
- First version recorded
- Jun 23, 2026
- Size
- 16,608 bytes
- Repository stars
- 503
- License
- a license file GitHub does not identify
End-to-end Proteina-Complexa design pipeline driver. Reach for this skill whenever the user wants to "design a binder", "design binders for X", "run complexa design", "de novo binder", "PDL1 binder", "TrkA binder", "design proteins for target", "protein binder design", "ligand binder", "design a small-molecule binder", "ATP-binding protein", "AME motif scaffolding", "scaffold a motif near a ligand", "motif + ligand design", "enzyme scaffolding", "flow matching protein design…
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
# Complexa Design Skill Drive the full four-stage `complexa design` pipeline: generate (flow matching + search) -> filter (top-N by reward) -> evaluate (refold with AF2/RF3) -> analyze (success rate, FoldSeek/MMseqs diversity). Pick the right pipeline config for the design intent, validate the run upfront so the user does not discover a missing ckpt mid-folding, run it, and emit a replayable manifest + per-design success CSV. ## What this skill enables - Protein binder design for protein targets (AF2 reward + ColabDesign refold). - Ligand binder design for small-molecule targets (RF3 reward + RF3 refold). - AME motif scaffolding with ligand context (motif + ligand features, RF3). - Search-based optimization: single-pass, best-of-n, beam-search, fk-steering, mcts. - Refold backends: ColabDesign (AF2), RF3, Boltz2, ESMFold (fast iteration). - Pass-rate + diversity analysis with per-`result_type` thresholds. ## Step 1: Pre-flight Always run the shared preflight before launching a design — generation needs the GPU and the right checkpoint, evaluation needs AF2/RF3 weights and tool binaries. Bail early if the host cannot run the chosen pipeline. ```bash …
Read the whole file at its exact version.
How to install
mdr add nvidia-bionemo/bionemo-agent-toolkit/complexa-design@sha256:4a31a28001b38635The line at the top of this page pins the label git:20261016.a6eced5, 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_6rlp4aymjaezj75g)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between Jun 23, 2026 and Oct 16, 2026, about one every 58 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20261016.a6eced5 latest | 2026-10-16 | a6eced5 | 16,608 B | A | view · diff |
| git:20260812.47315cc | 2026-08-12 | 47315cc | 16,532 B | A | view · diff |
| git:20260623.4e8fda7 | 2026-06-23 | 4e8fda7 | 19,821 B | A | view |
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 (16608 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_6rlp4aymjaezj75g GET https://markdownregistry.com/api/v1/resolve?ref=nvidia-bionemo/bionemo-agent-toolkit/complexa-design GET https://markdownregistry.com/api/v1/blob/4a31a28001b38635dcf946f3d1f69979b4690973131b9aef547a12f16e1a7b9e
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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