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foldseek-structural-search

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Performs 3D structural searches of proteins against various databases (PDB, AlphaFold, CATH, MGnify, etc.) using the Foldseek API. Use ONLY when the user provides a physical 3D coordinate file (.cif, .mmcif, or .pdb) and wants to find structurally similar proteins. Do NOT use if the user only provides a protein sequence, gene name, or UniProt ID.

skills/foldseek_structural_search/SKILL.md

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Last checked
Nov 9, 2026

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3,440
Repository last updated
Oct 23, 2026
License
Apache-2.0

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## Prerequisites

1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
    `uv` is installed and on PATH.
2.  **User Notification**: If .licenses/foldseek_structural_search_LICENSE.txt
    does not already exist in the workspace root directory then (1) prominently
    notify the user to check the terms at https://search.foldseek.com/search and
    https://github.com/steineggerlab/foldseek, then (2) create the file
    recording the notification text and timestamp.

## Goal

Submit a user-provided 3D protein structure file (`.cif`, `.mmcif`, or `.pdb`)
to the Foldseek web server API to find structurally similar proteins. Report the
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