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Foldseek Structural Search

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3D protein structure alignment against large-scale database repositories.

What it does

Foldseek Structural Search grants your assistant the ability to perform remote structural homology queries. By analyzing physical 3D coordinate files, it identifies potential evolutionary or functional relatives within major protein databases. It processes the input and returns a structured table summarizing matches alongside relevant statistical alignment confidence metrics.

Installing this skill allows the assistant to move beyond text-based identifiers, focusing instead on the geometric arrangement of atoms. It generates persistent documentation in the workspace, ensuring that alignment findings remain available for further investigation or record-keeping.

When it earns its place

Reach for it when…

Use this skill when you have a local PDB, CIF, or mmCIF file and need to discover proteins with similar shapes to investigate unknown folds, infer protein function, or analyze potential structural homologs in established repositories like the AlphaFold Database or CATH.

Look elsewhere when…

Do not attempt to use this for queries involving amino acid sequences, gene names, or UniProt accession IDs, as it lacks the capacity to look up structures from these identifiers. It is also inappropriate for evaluating simple, sequence-only mutations or predicting structures from scratch.

What to say to use it

You never invoke a skill directly — the assistant picks it up when your request matches what it covers. These are the kinds of things that do that.

  • find proteins with a similar shape to this PDB file
  • compare this CIF structure against the AlphaFold database
  • search for structural homologs of my protein model
  • identify similar protein folds using this coordinate file

Install it

Install for all your projects

Copy the skill directory into your personal skills folder. Claude picks it up on its own the next time your request matches what it does — there is nothing to enable.

bash
git clone --depth 1 --branch main https://github.com/google-deepmind/science-skills.git /tmp/science-skills
mkdir -p ~/.claude/skills
cp -r /tmp/science-skills/skills/foldseek_structural_search ~/.claude/skills/foldseek-structural-search

Install for one project only

Put it in the project's own skills folder instead, so it can be committed and shared with everyone working on that repository.

bash
cp -r /tmp/science-skills/skills/foldseek_structural_search .claude/skills/foldseek-structural-search

If a skill of the same name exists in both places, the personal one wins.

Installing on Claude.ai or through the API instead? The full guide covers every surface.

Pair it with an MCP server

Foldseek Structural Search changes how the work is done. These servers change what Claude can reach while doing it.

How skills and MCP servers differ →