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tooluniverse-protein-interactions

Analyze protein-protein interaction networks using STRING, BioGRID, and SASBDB databases.

1.7k|254|Updated Mar 3, 2025
Search Tags:#systems biology#network analysis#pathway enrichment#PPI network#biogrid#protein interactions#STRING database
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-protein-interactions
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-protein-interactions
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-protein-interactions
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-protein-interactions

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires tooluniverse.

What problem does it solve?

Researchers studying protein networks must manually query multiple databases, map identifiers, and interpret interaction evidence types, which is slow and error-prone. This Skill automates a 4-phase workflow—identifier mapping, network retrieval, enrichment analysis, and optional structural data lookup—so you can go from a list of gene names to a complete interaction network report in one step.

Core Features & Use Cases

  • Identifier Mapping & Network Retrieval: Convert gene symbols or UniProt IDs to STRING identifiers, then retrieve interaction networks with confidence scores from STRING (14M+ proteins) or curated experimental data from BioGRID (2.3M+ interactions).
  • Functional Enrichment Analysis: Identify enriched GO terms, KEGG/Reactome pathways, and test whether your protein set forms a statistically significant functional module via PPI enrichment p-values.
  • Structural & Extended Analysis: Optionally query SASBDB for SAXS/SANS solution structures, plus extended tools for signaling pathways (OmniPath, Reactome), druggability (DGIdb), and clinical evidence (CIViC).
  • Use Case: Given proteins TP53, MDM2, ATM, CHEK2, and CDKN1A, the Skill maps all identifiers, retrieves 10 high-confidence interactions, finds 374 enriched GO terms, and confirms the set forms a functional module (p=1.99e-06).

Quick Start

Ask the AI to analyze the interaction network for your list of proteins, for example: analyze the protein interaction network for TP53, MDM2, and ATM in human with high confidence interactions.

Frequently Asked Questions about tooluniverse-protein-interactions

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I analyze a protein interaction network with STRING?▼

Provide a list of gene symbols or UniProt IDs and a species taxonomy ID (default 9606 for human). The workflow maps identifiers with STRING_map_identifiers, retrieves the network with STRING_get_network, and runs functional and PPI enrichment analysis.

What is the difference between STRING and BioGRID interaction data?▼

STRING combines predicted and experimental functional associations with confidence scores, while BioGRID contains only experimentally validated, literature-curated interactions. A high STRING combined score does not prove physical binding—check the escore (experimental score) or BioGRID evidence for direct binding.

Does BioGRID require an API key?▼

Yes, all BioGRID tools require the BIOGRID_API_KEY environment variable, obtainable free from the BioGRID website. STRING and SASBDB tools work without any API key, so STRING serves as the primary source with BioGRID as an optional fallback.

Why does my protein network analysis find no interactions?▼

No interactions usually means the confidence threshold is too high or protein names are misspelled (they are case-sensitive). Lower the confidence_score parameter to 0.4 for exploratory analysis and verify gene symbols map correctly in the identifier mapping phase.

How many proteins do I need for enrichment analysis?▼

Functional enrichment and PPI enrichment require a minimum of 3 proteins for meaningful statistical analysis, with 10-50 proteins being ideal. Single-protein queries can still retrieve interaction partners but skip the enrichment phases.

Why does ToolUniverse print many error loading tools messages?▼

These messages are a known ToolUniverse framework limitation where it reloads all tool categories on every call and reports missing optional files. They do not affect results; filter them by piping output through grep -v "Error loading tools".

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