pdb-database
Installation
SKILL.md
PDB Database
Why no SDK? The
rcsb-apiPython SDK is convenient sugar over three public, no-auth REST endpoints (search.rcsb.org,data.rcsb.org,files.rcsb.org). When the SDK is unavailable, every operation can be reproduced with plainrequestsand a small JSON payload. This SKILL.md uses the REST path throughout so the code runs in any environment withrequestsinstalled.
Overview
RCSB PDB is the worldwide repository for 3D structural data of biological macromolecules with 200,000+ experimentally determined structures. Programmatic access is via three free, no-auth endpoints:
| API | Base URL | Method | Purpose |
|---|---|---|---|
| Search | https://search.rcsb.org/rcsbsearch/v2/query |
POST JSON |
Find PDB IDs by text, attribute filters, sequence, or 3D similarity |
| Data | https://data.rcsb.org/graphql |
POST GraphQL |
Retrieve structured metadata (entries, polymer entities, assemblies, ligands) |
| Files | https://files.rcsb.org/download/{id}.{format} |
GET |
Download coordinate files (mmCIF, PDB, FASTA) |
Use this skill for programmatic structural biology queries, drug target analysis, and protein family comparisons.