AlterLab PDB Access
技能 已验证 活跃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. 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.
功能
- 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
使用场景
- 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
非目标
- Performing molecular dynamics simulations
- Designing novel protein structures from scratch
- Replacing specialized molecular visualization software
工作流
- 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)
实践
- API Integration
- Data Retrieval
- Bioinformatics Data Handling
先决条件
- Python 3.8+
- uv pip install rcsb-api
安装
npx skills add AlterLab-IEU/AlterLab-Academic-Skills通过 npx 运行 Vercel skills CLI(skills.sh)— 需要本地安装 Node.js,以及至少一个兼容 skills 的智能体(Claude Code、Cursor、Codex 等)。前提是仓库遵循 agentskills.io 格式。
质量评分
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