Search RCSB PDB for protein structures and download PDB files.
npx skills add https://github.com/IDEA-XL/MolClaw --skill query-pdb-idea-xl
Please help me install this Agent Skill. Skill: query-pdb Source: https://github.com/IDEA-XL/MolClaw/tree/main/.claude/skills/query-pdb Command: npx skills add https://github.com/IDEA-XL/MolClaw --skill query-pdb-idea-xl
This skill helps researchers quickly locate and access experimental protein structures from the RCSB Protein Data Bank (PDB), covering X-ray, cryo-EM, and NMR data, and makes it easy to obtain corresponding PDB files.
Ask me to fetch experimental structures for a given protein or PDB ID, and I will search the PDB, retrieve details, and download the PDB file.
High-intent search queries and answers about installing and using this skill.
To download protein structures from the RCSB PDB, you can search using keywords, PDB IDs, genes, or organisms. The tool retrieves entry details like experimental method and resolution, then directly downloads the PDB files to your workspace for analysis.
You can find high-resolution crystal structures by searching the PDB with your target protein's keywords or gene name. The search returns entry details including experimental method and resolution, allowing you to identify and download the highest quality structures available.
Yes, you can retrieve cryo-EM and NMR experimental data from the Protein Data Bank. The search covers multiple experimental methods, returning the specific method used and its resolution for each entry, which you can then download as a PDB file.
The best way to get PDB file paths for downstream structural analysis is to search for entries by PDB ID or keyword. The tool downloads the PDB files directly to your workspace and returns the exact file paths alongside a summary of the experimental methods.
No, searching the RCSB PDB does not require a specific PDB ID. You can perform text searches using keywords, gene names, or organisms to discover relevant experimental protein structures, retrieve their details, and download the corresponding files.
To compare experimental methods and resolution for multiple PDB entries, search for your target protein using relevant keywords. The tool retrieves and summarizes the experimental method and resolution for each matching entry, enabling direct comparison before you download the PDB files.
yf8578Query the RCSB PDB database for protein structures by text, gene name, or method.
rubenslivSearch, download, and analyze PDB structures via REST or GraphQL.
awslabsStandardize protein structure analysis workflows with PDB/mmCIF parsing, RMSD superposition, and binding pocket detection.
felixboehmRetrieve AlphaFold-predicted 3D protein structures by UniProt ID.
