NVIDIA BioNeMo Agent Toolkit

Turn any agent into a life science expert with NVIDIA BioNeMo skills.

Protein folding, molecular docking, generative chemistry, genomics analysis, protein design, and biomarker discovery — a decade of NVIDIA life sciences libraries, tools, and models, packaged as ready-to-call agent skills.

Each skill gives a coding or scientific agent structured instructions, scripts, and references to select a tool, prepare inputs, run it, inspect outputs, and explain results — across both single tasks and multi-step scientific workflows.

Install

Skills install with the skills CLI:

# interactive — pick a skill + install destination
npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit

# one skill, no prompts
npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill boltz2-nim --yes

# target a specific agent (repeatable)
npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill boltz2-nim --agent claude-code
npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill boltz2-nim --agent codex

# browse the catalog without installing
npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --list

The repo also ships self-hosted plugin marketplaces:

• Codex: .agents/plugins/marketplace.json
• Claude Code: .claude-plugin/marketplace.json so the bionemo-agent-toolkit plugin installs through each agent's native plugin flow as well. Skills are also discoverable by partner harnesses directly from the repo.

What's here

workflows/            Multi-step meta-skills that compose the skills below
  generative_protein_binder_design/ RFdiffusion -> ProteinMPNN -> OpenFold3

nim-skills/           BioNeMo NIM skills (OpenFold, Boltz-2, DiffDock, GenMol,
                      RFdiffusion, ProteinMPNN, Evo2, MSA-Search, MolMIM, ...)
open-models-skills/   Open-model skills (Proteina-Complexa, KERMT, ...)
library-skills/       CUDA-X library skills (nvMolKit, cuEquivariance, parabricks, ...)

plugins/bionemo-agent-toolkit/   Generated installable plugin (claude + codex
                                 manifests + a copy of every catalog skill)
.claude-plugin/marketplace.json  Claude Code marketplace
.agents/plugins/marketplace.json Codex marketplace
skills.sh.json                   `npx skills add` catalog grouping

Every skill is a directory with a SKILL.md (YAML frontmatter + instructions), optional references/, and optional scripts/.

License

This project is dual-licensed:

• Source code (scripts, tests, build tooling): Apache-2.0
• Skills and documentation (SKILL.md, workflows, READMEs): CC-BY-4.0

See LICENSE for the full dual-license statement. Individual skills may reference third-party data sources with their own terms; consult each skill's references and the NOTICE file.