Search protein structures against PDB and AlphaFold databases with Foldseek.
npx skills add https://github.com/adaptyvbio/protein-design-skills --skill foldseek
Please help me install this Agent Skill. Skill: foldseek Source: https://github.com/adaptyvbio/protein-design-skills/tree/main/skills/foldseek Command: npx skills add https://github.com/adaptyvbio/protein-design-skills --skill foldseek
This skill automates structure similarity search for proteins using Foldseek.
It supports locating homologous structures, remote homologs, and clustering across large structure databases such as PDB and AlphaFold DB, enabling rapid assessment of design plausibility.
Use Foldseek to search a query structure against a database: foldseek easy-search query.pdb pdb100 results.m8 tmp/ --format-output query,target,pident,alnlen,evalue,bits
High-intent search queries and answers about installing and using this skill.
Detecting remote homologs relies on protein structure similarity rather than sequence alone. Foldseek compares a query structure against large databases to identify distant evolutionary relationships that sequence-based searches often miss.
The best way to cluster large sets of protein structures is by using Foldseek for rapid structural similarity ranking. It groups proteins into clusters based on fold similarity, enabling quick assessment of design plausibility across extensive structural datasets.
You do not necessarily need a local Foldseek installation to perform a structure similarity search. The task supports both local command-line interface usage and web access, depending on your available environment and scale requirements.
You can configure e-value and minimum sequence identity thresholds for homology searches by setting specific parameters. Foldseek accepts configurable parameters such as min-seq-id and e-value to filter structural similarity results.
A structural homology search compares 3D protein folds to identify similarities, whereas sequence-based detection relies on amino acid alignments. Using Foldseek allows you to find remote homologs across PDB and AlphaFold databases that sequence searches cannot detect.
zongtingweiSearch protein structure databases for homologous structures using Foldseek.
google-deepmindSearch protein 3D structures against Foldseek databases and write Markdown and JSON results.
sanand0Retrieve AlphaFold protein structures and analyze pLDDT/PAE metrics via API or Google Cloud bulk access.
PharMolixRetrieve proteins with similar structure or sequence from UniProt IDs, PDB IDs, FASTA strings, or PDB files.
