Individual skill
tooluniverse-protein-interactions
Protein-protein interaction (PPI) network analysis — STRING (predicted + experimental), BioGRID (curated), SASBDB (small-angle scattering), Complex Portal (curated complex membership and stoichiometry, includes CORUM data). Distinguishes physical interactions (binding) from functional associations (co-expression, co-regulation). Use for interactome queries, complex partner identification, curated complex composition lookup, and pathway-level interaction analysis.
plugins/tooluniverse/skills/tooluniverse-protein-interactions/SKILL.md
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.env.templateasset · 499 bytesDESCRIPTION_UPDATE_COMPLETE.mddoc · 1,945 bytesDESCRIPTION_UPDATE_PROGRESS.mddoc · 5,084 bytesDOMAIN_ANALYSIS.mddoc · 13,105 bytesKNOWN_ISSUES.mddoc · 3,505 bytesPHASE2_DISCOVERIES.mddoc · 7,372 bytesQUICK_START.mddoc · 4,101 bytesSKILL.mdcore · 17,244 bytesSKILL.mdcore · 17,244 bytesSKILL.mdcore · 17,244 bytesSKILL.mdcore · 17,244 bytesTOOL_DESCRIPTION_OPTIMIZATION.mddoc · 22,101 bytespython_implementation.pyruns · 14,741 bytes
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# 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 |
|----------|----------|---------|---------|