Query RCSB PDB for protein structures and metadata via REST APIs.
npx skills add https://github.com/Runchuan-BU/BioClaw --skill query-pdb
Please help me install this Agent Skill. Skill: query-pdb Source: https://github.com/Runchuan-BU/BioClaw/tree/main/.claude/skills/query-pdb Command: npx skills add https://github.com/Runchuan-BU/BioClaw --skill query-pdb
This Skill lets you quickly find and retrieve experimental 3D protein structures and associated metadata from the RCSB Protein Data Bank, removing the need for manual web searches and manual entry inspection.
Ask the query-pdb skill to search for "human ACE2" with method "ELECTRON MICROSCOPY" and return the top five PDB entries.
High-intent search queries and answers about installing and using this skill.
To download protein structures from the RCSB PDB, you can query by direct PDB ID or free text to retrieve entry details and downloadable PDB files over HTTPS. This provides immediate access to experimental 3D structure data for local analysis.
Yes, you can search for cryo-EM or X-ray structures by applying advanced filtered queries using gene name, organism, and experimental method. This narrows results to specific structural data entries derived from Electron Microscopy or X-Ray Diffraction.
Retrieving protein structure metadata like resolution and ligands is best done by querying the RCSB REST APIs. This returns listed entries detailing experimental methods, reported resolutions, and associated ligands without manual web inspection.
You can find specific PDB entries using free text queries with pagination support to manage large result sets. Querying the RCSB REST APIs over HTTPS lists matching entries while handling basic HTTP errors to ensure reliable data retrieval.
Yes, this tool provides downloadable PDB files for binding-site analysis by fetching entry details directly from the RCSB database. You can locate specific structures, compare reported resolutions, and download selected files for local visualization.
A limitation when searching for NMR protein structures is that queries rely on basic HTTP error handling and pagination, which may require multiple requests for large datasets. Searches are restricted to existing RCSB PDB entries filtered by Solution NMR methodology.
yf8578Query the RCSB PDB database for protein structures by text, gene name, or method.
biomaps-infraPredict molecular docking poses for protein-ligand interactions using diffusion models.
InternSciencePredicts ligand binding pockets in PDB proteins with confidence scores and docking boxes.
MDheweiResolve gene symbols to UniProt accessions and render domain maps.