Search and retrieve PDB structure data from the RCSB Protein Data Bank.
npx skills add https://github.com/swaruplab/operon --skill pdb-database-swaruplab
Please help me install this Agent Skill. Skill: pdb-database Source: https://github.com/swaruplab/operon/tree/main/src-tauri/protocols/pdb-database Command: npx skills add https://github.com/swaruplab/operon --skill pdb-database-swaruplab
PDB-database streamlines access to the RCSB Protein Data Bank by enabling quick searches, retrieval of structure metadata, and downloading structure files for downstream analysis.
Search for a structure by entry ID (e.g., 4HHB), fetch its entry data, and download its PDB file.
High-intent search queries and answers about installing and using this skill.
To download PDB structure files and retrieve metadata from the Protein Data Bank, search by entry ID, text, sequence, or structural similarity, then fetch coordinate files in PDB or mmCIF format along with associated assembly options.
Yes, you can batch fetch multiple structures and automate bioinformatics pipelines programmatically by accessing RCSB data through RESTful endpoints and GraphQL queries for integration into reproducible computational workflows.
Searching the RCSB PDB supports finding biological structures by text, sequence, or structural similarity to retrieve entry details like title, organism, resolution, and deposition date.
Retrieving PDB data requires specifying a file format before downloading coordinates, allowing you to choose between standard PDB format and mmCIF format for individual or batch structural workflows.
The best way to access RCSB PDB data for structural discovery is using programmatic APIs to query entries and download coordinate files, streamlining integration into downstream structural biology analysis pipelines.
qinyan-aiSearch and retrieve 3D structural data from the RCSB PDB.
MooseGoose0701Search and retrieve PDB/mmCIF coordinate files from RCSB PDB.
omar-A-hassanRetrieves protein structure entries and metadata from the RCSB PDB via APIs.
sanand0Parse FASTA, GenBank, and PDB files for molecular biology analysis.
