Search protein 3D structures against PDB and AlphaFold DB for similar folds and homologs.
npx skills add https://github.com/junior1p/ProteinClaw --skill foldseek-junior1p
Please help me install this Agent Skill. Skill: foldseek Source: https://github.com/junior1p/ProteinClaw/tree/main/skills/foldseek Command: npx skills add https://github.com/junior1p/ProteinClaw --skill foldseek-junior1p
Foldseek enables fast, structure-based similarity searches to detect homologs and similar folds that sequence-based methods may miss, streamlining scaffold discovery and novelty checks for protein designs.
Use the foldseek skill to search design.pdb against afdb50 and return the top 10 hits with alignment metrics and an e-value threshold of 0.001.
High-intent search queries and answers about installing and using this skill.
To find structural homologs, query a protein PDB file against databases like afdb50 and filter results using e-value and sequence identity thresholds.
Protein structure search detects similar folds and homologs that sequence-based methods often miss, enabling scaffold discovery and novelty checks for protein designs.
Yes, you can perform large-scale local searches against downloadable PDB databases, but you must configure adequate RAM and disk space to handle the data volume.
You can configure minimum sequence identity and e-value thresholds to tune your PDB structure search, prioritizing either sensitivity or specificity for your hits.
Yes, Foldseek supports motif scaffold discovery and novelty checks by searching clustered AlphaFold databases to find structural neighbors and verify if a design already exists.
Searching clustered protein structure databases locally demands significant RAM and disk space, making the web API a better alternative for quick, rate-limited queries.
robotlearning123Search and retrieve 3D protein and nucleic acid structures from RCSB Protein Data Bank.
Runchuan-BURun BLAST searches for DNA, RNA, or protein sequences in BioClaw.
zongtingweiSearch protein structure databases for homologous structures using Foldseek.
google-deepmindSearch protein sequence databases for homologues and infer functions.
