protein-interaction-network-analysis
Analyze protein-protein interaction networks using STRING, BioGRID, and SASBDB databases. Maps protein identifiers, retrieves interaction networks with confidence scores, performs functional enrichment analysis (GO/KEGG/Reactome), and optionally includes structural data. No API key required for core functionality (STRING). Use when analyzing protein networks, discovering interaction partners, identifying functional modules, or studying protein complexes.
npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-protein-interactions --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Protein Interaction Network Analysis Comprehensive protein interaction network analysis using ToolUniverse tools. Analyzes protein networks through a 4-phase workflow: identifier mapping, network retrieval, enrichment analysis, and optional structural data. ## Features ✅ **Identifier Mapping** - Convert protein names to database IDs (STRING, UniProt, Ensembl) ✅ **Network Retrieval** - Get interaction networks with confidence scores (0-1.0) ✅ **Functional Enrichment** - GO terms, KEGG pathways, Reactome pathways ✅ **PPI Enrichment** - Test if proteins form functional modules ✅ **Structural Data** - Optional SAXS/SANS solution structures (SASBDB) ✅ **Fallback Strategy** - STRING primary (no API key) → BioGRID secondary (if key available) ## Databases Used | Database | Coverage | API Key | Purpose | |----------|----------|---------|---------| | **STRING** | 14M+ proteins, 5,000+ organisms | ❌ Not required | Primary interaction source | | **BioGRID** | 2.3M+ interactions, 80+ organisms | ✅ Required | Fallback, curated data | | **SASBDB** | 2,000+ SAXS/SANS entries | ❌ Not required | Solution structures | ## Quick Start ### Basic Usage ```python from tooluniverse import ToolUniverse f
- Features
- Databases Used
- Quick Start
- Basic Usage
- Expected Output
- Use Cases
- 1. Single Protein Analysis
- 2. Protein Complex Validation
- 3. Pathway Discovery
- 4. Multi-Protein Network Analysis
- 5. With BioGRID Validation
- 6. Including Structural Data
- Parameters
- analyzeproteinnetwork() Parameters
Install ToolUniverse (if not already installed) pip install tooluniverse Or with extras pip install tooluniverse[all] python your_script.py 2>&1 | grep -v "Error loading tools"
What does the protein-interaction-network-analysis skill do?
Analyze protein-protein interaction networks using STRING, BioGRID, and SASBDB databases. Maps protein identifiers, retrieves interaction networks with confidence scores, performs functional enrichment analysis (GO/KEGG/Reactome), and optionally includes structural data. No API key required for core functionality (STRING). Use when analyzing protein networks, discovering interaction partners, identifying functional modules, or studying protein complexes.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-protein-interactions --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.