protein-interaction-network-analysis

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.

Domain Reasoning: Interaction Type Clarification

When asked about protein interactions, ask: physical interaction (do they bind?) or functional interaction (do they affect the same pathway)? STRING combines both — a high combined_score does not mean physical binding. For physical binding evidence, check the experimental score (escore) specifically. A high tscore (text mining) or dscore (database) with a low escore suggests co-annotation or co-citation, not direct binding.

LOOK UP DON'T GUESS: protein interaction scores, experimental evidence types, and whether two specific proteins have known co-crystal structures. Use STRING escore and BioGRID experimental data — do not infer binding from pathway co-membership alone.

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

4-Phase Workflow

1. Identifier Mapping — STRING_map_identifiers(): validate protein names, get STRING IDs
2. Network Retrieval — STRING_get_network() (primary); BioGRID_get_interactions() (fallback, requires API key)

Parameters

Confidence Score Guidelines

Network Edge Fields (STRING)

Extended Analysis Tools

Tool-Specific Notes

IntAct Interaction Data

BioGRID Chemical Interactions

IntAct protein_name Alias

Domain Reasoning: Multimeric Assemblies & Binding Valency

Calculating Multimer Valency from Binding Data