pdb-database
Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
npx skills add LeonChaoX/qinyan-academic-skills --skill pdb-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# PDB Database ## Overview RCSB PDB is the worldwide repository for 3D structural data of biological macromolecules. Search for structures, retrieve coordinates and metadata, perform sequence and structure similarity searches across 200,000+ experimentally determined structures and computed models. ## When to Use This Skill This skill should be used when: - Searching for protein or nucleic acid 3D structures by text, sequence, or structural similarity - Downloading coordinate files in PDB, mmCIF, or BinaryCIF formats - Retrieving structural metadata, experimental methods, or quality metrics - Performing batch operations across multiple structures - Integrating PDB data into computational workflows for drug discovery, protein engineering, or structural biology research ## Core Capabilities ### 1. Searching for Structures Find PDB entries using various search criteria: **Text Search:** Search by protein name, keywords, or descriptions ```python from rcsbapi.search import TextQuery query = TextQuery("hemoglobin") results = list(query()) print(f"Found {len(results)} structures") ``` **Attribute Search:** Query specific properties (organism, resolution, method, etc.) ```python from rcsb
- Overview
- When to Use This Skill
- Core Capabilities
- 1. Searching for Structures
- 2. Retrieving Structure Data
- 3. Downloading Structure Files
- 4. Working with Structure Data
- 5. Batch Operations
- Python Package Installation
- Common Use Cases
- Drug Discovery
- Protein Engineering
- Structural Biology Research
- Education and Visualization
Current recommended package uv pip install rcsb-api For legacy code (deprecated, use rcsb-api instead) uv pip install rcsbsearchapi
What does the pdb-database skill do?
Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill pdb-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.