AlterLab PDB Access
Skill Verified ActiveAccess 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.
Features
- 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
Use Cases
- 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
Non-Goals
- 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)
Practices
- API Integration
- Data Retrieval
- Bioinformatics Data Handling
Prerequisites
- Python 3.8+
- uv pip install rcsb-api
Installation
npx skills add AlterLab-IEU/AlterLab-Academic-SkillsRuns the Vercel skills CLI (skills.sh) via npx — needs Node.js locally and at least one installed skills-compatible agent (Claude Code, Cursor, Codex, …). Assumes the repo follows the agentskills.io format.
Quality Score
VerifiedTrust Signals
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