Individual skill
pdb-database
Access the RCSB Protein Data Bank (PDB) to search, download, and programmatically retrieve 3D macromolecular structures and metadata; use when you need structure discovery (text/sequence/3D similarity) or automated structural data ingestion for structural biology and drug discovery workflows.
scientific-skills/Evidence Insight/pdb-database/SKILL.md
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- bioinformatics Repository topic
- computational-biology Repository topic
- data-analysis Repository topic
- ai Repository topic
- biology Repository topic
- cancer-genomics Repository topic
- data-visualization Repository topic
- differential-expression Repository topic
- genomics Repository topic
- medical Repository topic
- data Derived category
- data-databases Derived category
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SKILL.mdcore · 6,242 bytesSKILL.mdcore · 6,242 bytesSKILL.mdcore · 6,242 bytesSKILL.mdcore · 6,242 bytesSKILL.mdcore · 6,242 bytespdb-database_audit_result_v1.jsonasset · 11,774 bytesreferences/api_reference.mddoc · 16,051 bytes
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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)
## When to Use
Use this skill when you need to:
- Find protein/nucleic acid 3D structures by **keywords**, **organism**, **experimental method**, or **resolution**.
- Identify related structures via **sequence similarity** (e.g., homolog search for modeling).
- Identify related structures via **3D structure similarity** (e.g., fold-level comparisons).
- **Download coordinates** (PDB/mmCIF) for downstream analysis, visualization, docking, or modeling.
- Run **batch retrieval** of metadata/coordinates to feed pipelines in drug discovery, protein engineering, or structural bioinformatics.
## Key Features
- Text and attribute-based search over RCSB PDB entries.