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Generate and optimize molecules with MolMIM v1.0.0

Use this resource to generate and optimize small molecules around a seed SMILES with MolMIM

New

  • 424 downloads
  • 146 likes
  • 209 saves

Free

Install with the CLI

In a terminal, from the folder you want:

npx --yes palatekit@latest install small-molecule-latent-optimization-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 picks the mode (hosted API or local Docker), prepares the seed SMILES, runs sampling around it or CMA-ES optimization, then validates the molecules produced. The target properties are QED or plogP.

Mostly picked by

Updated November 2, 2026

Card for the “Generate and optimize molecules with MolMIM” 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, optimization flow and procedure
  • references/parameters.md : generation and sampling settings
  • references/validation.md : SMILES and property checks

Good fit for

  • You want variants of a seed molecule
  • You optimize the QED of candidates

Not for

    Tags

    • molmim
    • molecules
    • latent space
    • optimization
    • qed

    About

    You say

    “Optimize this seed molecule with MolMIM to raise its QED.”

    Card for the “Generate and optimize molecules with MolMIM” 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 optimize small molecules around a seed SMILES with MolMIM
    3. Review and adjust the result

    Content preview

    Files

    • BENCHMARK.md7 KB
    • config/skillspector-baseline.yml0.9 KB
    • evals/config.yml0.1 KB
    • evals/evals.json6.2 KB
    • evals/trigger_evals.json1.8 KB
    • LICENSE11.3 KB
    • NOTICE-PALATEKIT.md0.5 KB
    • references/api.md4.6 KB
    • references/examples.md2.2 KB
    • references/parameters.md2 KB
    • references/science.md2.3 KB
    • references/validation.md1.8 KB
    • skill-card.md4.1 KB
    • SKILL.md7.6 KB
    • skill.oms.sig6.3 KB

    Origin and licence

    Listed unmodified

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

    Notice

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

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