Can I run searches locally or do I need internet access?

Both options are available; you can use the Foldseek web server for quick queries or install Foldseek locally via Conda for private, large-scale database searches.

Which databases are supported by this skill?

The skill supports searching against PDB100, AlphaFold DB (AFDB50), SwissProt structures, and CATH50 domains.

Why use Foldseek instead of BLAST?

Foldseek searches by 3D structure rather than sequence, allowing it to find remote homologs that share similar folds despite having low sequence identity that BLAST might miss.

Do I need a GPU to run the Foldseek skill?

No, Foldseek is highly optimized for CPU performance and does not require a GPU for structural searches, making it accessible on standard hardware.

What output format does the skill provide?

It provides a standard m8 tabular output containing query and target names, sequence identity, alignment length, E-values, and bit scores.

Foldseek Structure Search

Name: Foldseek Structure Search
Author: adaptyvbio

byadaptyvbio

•

Data Science & ML

Performs fast and sensitive 3D protein structure similarity searches across global databases like PDB and AlphaFold DB.

The Foldseek skill enables Claude to perform advanced protein structure analysis by identifying structural homologs that sequence-based methods like BLAST might miss. It provides a comprehensive interface for querying 3D structures against massive databases including PDB, AFDB50, and SwissProt. This skill is essential for protein engineers needing to find similar designs, check for structural novelty, or identify scaffolds for motif grafting using local CLI tools or high-speed web APIs.

Key Features

01High-speed 3D structural homology searching across millions of entries

02Advanced filtering options for E-value, sequence identity, and alignment type

0375 GitHub stars

04Flexible execution via local CLI, Python API, or rate-limited Web API

05Support for major databases including PDB100, AlphaFold DB, and SwissProt

06Remote homolog detection using optimized 3Di+AA structural alignments

Use Cases

01Verifying the structural novelty of a protein fold against the AlphaFold Database

02Discovering compatible structural scaffolds for motif grafting in protein engineering

03Identifying natural structural analogs for synthetic or de novo protein designs

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add adaptyvbio/protein-design-skills foldseek

For use in Claude.ai and ChatGPT

Download Skill