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Agent skill

Complexa Target

by NVIDIA-BioNeMo in NVIDIA-BioNeMo/bionemo-agent-toolkit

A skill your agent uses whenever the user wants to add, register, edit, list, show, or validate a Proteina-Complexa design target for any pipeline — protein binder (default), ligand binder, or AME /…

Custom licenceAuto-check: notesResearch & Science

Install Complexa Target

skills CLI
$ npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill complexa-target -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install NVIDIA-BioNeMo/bionemo-agent-toolkit complexa-target --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bionemo-agent-toolkit/skills/complexa-target .claude/skills/complexa-target && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
complexa-target
GitHub stars
478
Token cost
~3.7k tokens
SKILL.md length
1,478 words
Files
3
Skills in repo
14
Repo updated
First seen
Licence
Custom licence

At a glance

A skill your agent uses whenever the user wants to add, register, edit, list, show, or validate a Proteina-Complexa design target for any pipeline — protein binder (default), ligand binder, or AME /…

  • Works in 4 steps: Decide the target type → Gather required info → Verify → …
  • The user wants to add
  • SKILL.md covers Preferred path: edit the YAML…, What this skill enables, Step 1: Decide the target type and Step 2: Gather required info, plus 7 more sections
  • Calls rg

What it does

Complexa Target is an agent skill from NVIDIA-BioNeMo/bionemo-agent-toolkit. Use this skill whenever the user wants to add, register, edit, list, show, or validate a Proteina-Complexa design target for any pipeline — protein binder (default), ligand binder, or AME / enzyme scaffolding. Triggers include "add a target", "define a new target for binder design", "register a hotspot", "set up a PDL1 binder target", "ligand binder pocket", "SMILES target", "AME task", "enzyme motif", "M00241nzy", "complexa target add", "complexa target show", "configure target X", "what targets are available"…

Its SKILL.md is about 3.7k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files (for example `evals/evals.json` and `reference/target_schema.md`).

It sits in Research & Science, covering Drug discovery and cheminformatics and Project scaffolding. The repository describes itself as: Turn any agent into a life science expert with NVIDIA BioNeMo skills.

When your agent uses it

  • The user wants to add
  • Validate a Proteina-Complexa design target for any pipeline — protein binder (default)
  • AME / enzyme scaffolding
  • Include add a target

Example prompts

  • “add a target”
  • “define a new target for binder design”
  • “register a hotspot”
  • “/complexa-target”

Requirements

  • Python 3
  • Pre-approved tools (allowed-tools): Bash, Read, Write, AskUserQuestion

Workflow steps

4 steps, taken from the step headings in SKILL.md.

  1. Decide the target type
  2. Gather required info
  3. Verify
  4. Emit artifact

What it can do on your machine

Read from SKILL.md and the folder at commit 2113472. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves these tools, so the agent can use them without asking each time:

    • Bash
    • Read
    • Write
    • AskUserQuestion

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Shell commands in SKILL.md call:

    • rg

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Complexa Target loads about 3.7k tokens when it runs. Until then it costs about 214 tokens; SKILL.md has 1,478 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~214
When it runs · the whole SKILL.md, loaded when a task matches
~3.7k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check: notes

The automated check noted patterns worth knowing about, such as sudo or a known installer.

  • NotePre-approves every shell command (allowed-tools: Bash)SKILL.md
    allowed-tools: Bash, Read, Write, AskUserQuestion

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 1,478 words (~3,712 tokens).

“Add or edit a design target in Proteina-Complexa. Targets live in three YAML files, one per complexa design pipeline:”

— opening of SKILL.md by NVIDIA-BioNeMo, Custom licence
name
complexa-target
allowed-tools
Bash, Read, Write, AskUserQuestion

Read the full SKILL.md on GitHub

Files

SKILL.md and 2 other files in skills/bionemo-agent-toolkit/skills/complexa-target of NVIDIA-BioNeMo/bionemo-agent-toolkit.

  • SKILL.md
  • evals/evals.json
  • reference/target_schema.md

Open the folder on GitHubat commit 2113472

Compare with similar skills

Complexa Target next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Complexa Target compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Complexa Target this skillNVIDIA-BioNeMo/bionemo-agent-toolkit478—~3.7kAutomated safety check: NotesCustom licence
Bio Shape SimilarityGPTomics/bioSkills1.2k2 repos~3.9kAutomated safety check: PassMIT
MolecodeAtomFlow-AI/MoleCode305—~1.9kAutomated safety check: PassMIT
Drug DiscoveryTommy-yw/RunbookHermes5461 repos~2.3kAutomated safety check: PassMIT
DiffDock Molecular DockingK-Dense-AI/scientific-agent-skills48k1 repos~3kAutomated safety check: NotesMIT
Biomedical Analysis Dispatchxjtulyc/MedgeClaw6171 repos~2kAutomated safety check: PassNone

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More from NVIDIA-BioNeMo/bionemo-agent-toolkit

All 14 skills in this repo

  • Complexa Binder Design

    NVIDIA-BioNeMo/bionemo-agent-toolkit

    Run a complete protein binder design campaign with NVIDIA Proteina-Complexa: resolve a target structure and hotspots from a name/sequence/PDB, co-design binder sequence+structure with reward-guided…

    478 GitHub stars~3.1k tokensUpdated yesterday
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  • Parabricks

    NVIDIA-BioNeMo/bionemo-agent-toolkit

    Route NVIDIA Parabricks pbrun tools, assess GPU/runtime readiness, and provide version-aware command guidance for FASTQ/BAM processing, RNA-seq, variant calling, BAM QC, and GVCF workflows.

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  • Protein Binder Design

    NVIDIA-BioNeMo/bionemo-agent-toolkit

    Orchestrate an end-to-end de novo protein binder design campaign against a protein target by composing BioNeMo NIM skills.

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  • Cuequivariance

    NVIDIA-BioNeMo/bionemo-agent-toolkit

    Build and debug cuEquivariance irreps, custom Irrep subclasses, Clebsch-Gordan tensor products, and equivariant or segmented polynomials.

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  • Genomics Workflow Acceleration

    NVIDIA-BioNeMo/bionemo-agent-toolkit

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  • Complexa Design

    NVIDIA-BioNeMo/bionemo-agent-toolkit

    End-to-end Proteina-Complexa design pipeline driver. An agent skill from NVIDIA-BioNeMo/bionemo-agent-toolkit.

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Categories

Questions about Complexa Target

What does Complexa Target do?

A skill your agent uses whenever the user wants to add, register, edit, list, show, or validate a Proteina-Complexa design target for any pipeline — protein binder (default), ligand binder, or AME /…. Complexa Target is an agent skill from NVIDIA-BioNeMo/bionemo-agent-toolkit. Use this skill whenever the user wants to add, register, edit, list, show, or validate a Proteina-Complexa design target for any pipeline — protein binder (default), ligand binder, or AME / enzyme scaffolding.

When should I use Complexa Target?

Complexa Target fits situations like: the user wants to add; validate a Proteina-Complexa design target for any pipeline — protein binder (default); AME / enzyme scaffolding; include add a target.

How do I install Complexa Target in Claude Code?

Run `npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill complexa-target -a claude-code`. Or copy the skill folder (skills/bionemo-agent-toolkit/skills/complexa-target in NVIDIA-BioNeMo/bionemo-agent-toolkit) into .claude/skills/complexa-target in your project. Claude Code loads it when a task matches its description.

How do I install Complexa Target in Codex?

Run `npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill complexa-target -a codex`. Or copy the skill folder (skills/bionemo-agent-toolkit/skills/complexa-target in NVIDIA-BioNeMo/bionemo-agent-toolkit) into .agents/skills/complexa-target in your project. Codex loads it when a task matches its description.

Can I use Complexa Target in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill complexa-target -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/complexa-target, .gemini/skills/complexa-target, .github/skills/complexa-target and .opencode/skills/complexa-target in your project.

What does Complexa Target need to run?

Going by SKILL.md and its folder, Complexa Target needs the command-line tools its instructions call (rg). Our summary lists: Python 3. Its frontmatter pre-approves these tools: Bash, Read, Write, AskUserQuestion.

Does Complexa Target access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Complexa Target safe to install?

Our automated static check of SKILL.md found notes only (pre-approves every shell command (allowed-tools: bash)), nothing it rates as a warning. It is not a guarantee. Review the folder before installing.

What licence does Complexa Target use?

Complexa Target has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.

How many tokens does Complexa Target use?

About 3.7k tokens (SKILL.md is roughly 15k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Complexa Target?

Skills that share tags, products or a category with Complexa Target: Bio Shape Similarity (GPTomics/bioSkills, 1.2k stars), Molecode (AtomFlow-AI/MoleCode, 305 stars), Drug Discovery (Tommy-yw/RunbookHermes, 546 stars) and DiffDock Molecular Docking (K-Dense-AI/scientific-agent-skills, 48k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Complexa Target?

NVIDIA-BioNeMo (a GitHub organization) maintains it in NVIDIA-BioNeMo/bionemo-agent-toolkit, which has 478 GitHub stars. The repository holds 14 skills in this directory. The repository was last updated on October 6, 2026.

Source: NVIDIA-BioNeMo/bionemo-agent-toolkit on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.