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Generate candidate molecules with GenMol v1.0.0

Use this resource to generate and rank candidate molecules from a scaffold or motif

New

  • 314 downloads
  • 223 likes
  • 113 saves

Free

Install with the CLI

In a terminal, from the folder you want:

npx --yes palatekit@latest install de-novo-molecule-generation-nim

With no option, the skill goes to ~/.agents/skills/; add --agent claude-code (or codex, cursor…) to target an agent.

First time: connect the CLI with

npx --yes palatekit@latest login

The agent converts your structures to SAFE notation (not ordinary SMILES), runs generation, then ranks results by QED or LogP. It chooses between the hosted API and local Docker.

Mostly picked by

Updated November 2, 2026

Card for the “Generate candidate molecules with GenMol” skill

Details

Works in
Install guides
Generates with
Your agent's model
Licence
CC-BY-4.0

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What you get

  • SKILL.md : modes, SAFE notation and procedure
  • references/parameters.md : settings and their effects
  • references/validation.md : chemical and artifact checks

Good fit for

  • You want new molecules around a known scaffold
  • You optimize an existing candidate while fixing a motif

Not for

    Tags

    • genmol
    • molecules
    • safe
    • chemistry
    • generation

    About

    You say

    “Decorate this scaffold with GenMol and rank the molecules by QED.”

    Card for the “Generate candidate molecules with GenMol” skill

    Skill published by nvidia under the CC-BY-4.0 license, delivered in its original version.

    Show more

    How to use it

    1. Install the skill in your agent's skills folder
    2. Ask your agent to generate and rank candidate molecules from a scaffold or motif
    3. Review and adjust the result

    Content preview

    Files

    • BENCHMARK.md7.2 KB
    • config/skillspector-baseline.yml0.3 KB
    • evals/config.yml0.1 KB
    • evals/evals.json10.6 KB
    • evals/trigger_evals.json2.2 KB
    • LICENSE11.3 KB
    • NOTICE-PALATEKIT.md0.5 KB
    • references/api.md7 KB
    • references/examples.md1.7 KB
    • references/parameters.md1.1 KB
    • references/science.md1.5 KB
    • references/validation.md1.2 KB
    • skill-card.md4.3 KB
    • SKILL.md5.4 KB
    • skill.oms.sig6.3 KB

    Origin and licence

    Listed unmodified

    Author
    nvidia
    Source
    github.com/nvidia/skills/tree/ca116d60beafe1b4459f0ab790b7b450912c56b0/skills/bionemo-genmol-nim
    Licence
    CC-BY-4.0

    Notice

    « genmol-nim » (nvidia, CC-BY-4.0) livré dans sa version d'origine : fiche en français et en anglais par PalateKit.

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