AlterLab PDB Access
Skill Verifiziert AktivAccess 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. Part of the AlterLab Academic Skills suite.
To provide researchers with a powerful tool for accessing and analyzing structural data from the RCSB PDB database, facilitating drug discovery, protein engineering, and structural biology research.
Funktionen
- Search structures by text, sequence, or structure similarity
- Download coordinate files in PDB, mmCIF, and BinaryCIF formats
- Retrieve detailed structural metadata and experimental information
- Utilize a comprehensive Python API for programmatic access
- Integrate with computational workflows for research and analysis
Anwendungsfälle
- Searching for protein structures of drug targets
- Downloading and analyzing coordinates for molecular modeling
- Retrieving experimental details and quality metrics for published structures
- Performing batch operations to gather data for multiple PDB entries
Nicht-Ziele
- Performing molecular dynamics simulations
- Designing novel protein structures from scratch
- Replacing specialized molecular visualization software
Workflow
- Define search criteria (text, sequence, structure)
- Execute search query using `rcsbapi.search`
- Retrieve PDB IDs from search results
- Fetch structure data or download coordinate files using `rcsbapi.data`
- Parse and analyze downloaded data with appropriate libraries (e.g., BioPython)
Praktiken
- API Integration
- Data Retrieval
- Bioinformatics Data Handling
Voraussetzungen
- Python 3.8+
- uv pip install rcsb-api
Installation
npx skills add AlterLab-IEU/AlterLab-Academic-SkillsFührt das Vercel skills CLI (skills.sh) via npx aus — benötigt Node.js lokal und mindestens einen installierten skills-kompatiblen Agent (Claude Code, Cursor, Codex, …). Setzt voraus, dass das Repo dem agentskills.io-Format folgt.
Qualitätspunktzahl
VerifiziertVertrauenssignale
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