Individual skill
biopython-structure
Use Bio.PDB to parse and analyze protein structures (PDB/mmCIF) for structural bioinformatics tasks; use when you need structure parsing, geometry calculations, or structural comparison/superposition.
scientific-skills/Data Analysis/biopython-structure/SKILL.md
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- bioinformatics Repository topic
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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)
# biopython-structure
## When to Use
- You need to parse **PDB** or **mmCIF** files and access the structure hierarchy (model → chain → residue → atom).
- You want to compute **geometric measurements** such as distances, bond angles, and dihedral angles between atoms/residues.
- You need **neighbor searches** (e.g., find residues/atoms within a cutoff) for contact analysis or local environment inspection.
- You want to perform **structural comparison**, including alignment/superposition and RMSD-style evaluation.
- You need to **extract, modify, and save** structures (e.g., subset chains/residues and write back to PDB/mmCIF).
## Key Features
- **Structure parsing** for PDB/mmCIF using `Bio.PDB` parsers.