foldseek

Name: foldseek
Availability: InStock
Author: zongtingwei

Search protein structure databases for homologous structures using Foldseek.

25|5|Updated Mar 22, 2026

Search Tags:#bioinformatics #pdb #structure-search #protein-design #foldseek #structure-homology #afdb

Ready to run

npx skills add https://github.com/zongtingwei/Bioclaw_Skills_Hub --skill foldseek-zongtingwei

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: foldseek
Source: https://github.com/zongtingwei/Bioclaw_Skills_Hub/tree/main/skills/protein-design/skills/foldseek
Command: npx skills add https://github.com/zongtingwei/Bioclaw_Skills_Hub --skill foldseek-zongtingwei

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Foldseek enables fast structure-based search to identify homologous or similar protein structures across large databases.

Core Features & Use Cases

Structure-based searches: search PDB/AFDB using Foldseek to identify similar structures.
Remote-homolog detection and clustering: identify remote homologs and cluster structures by similarity.
Use Case: Assess whether a design matches known scaffolds for design or scaffold transfer.

Quick Start

Provide a query structure and select a database to run a Foldseek search and obtain a ranked list of hits.

Frequently Asked Questions about foldseek

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I search for protein structural homologs across large databases like PDB and AlphaFold DB?▼

Structure-based search identifies homologous protein structures by comparing 3D conformations across databases like PDB and AlphaFold DB. Providing a query structure allows the system to rapidly retrieve a ranked list of similar structural hits.

What is the best way to detect remote homologs for protein design scaffolds?▼

Remote homolog detection for protein design scaffolds is best achieved through structural homology searching. By scanning against configured databases, this method uncovers distant evolutionary relationships that sequence-based searches often miss, providing viable scaffolds for design transfer.

Can I perform structure-based clustering on a local collection of protein structures?▼

Yes, you can perform structure-based clustering on a local collection of protein structures. By configuring the search to run against local databases, the tool groups structures by similarity, allowing for effective remote homolog detection and organization of local structural data.

Does Foldseek require local installation or can it use web services for structure search?▼

Foldseek requires either local installation or web services to run structure searches. This flexibility allows users to configure databases and execute searches locally for large-scale data privacy or via web services for accessible, on-demand structural homology retrieval.

How do I get detailed alignment metrics and hit lists from a structure search?▼

To get detailed alignment metrics and hit lists from a structure search, you provide a query structure and select a target database. The search outputs configurable formats containing comprehensive alignment data alongside a ranked list of structural hits.