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tooluniverse-immunology

Analyzes antibody-antigen interactions, immune repertoires, and autoimmune genetics using IEDB, IMGT, and SAbDab databases.

1.7k|254|Updated Mar 3, 2025
Search Tags:#antibody#immunology#drug safety#epitope#mhc binding#iedb#autoimmune
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-immunology
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-immunology
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-immunology
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-immunology

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Immunology research requires querying many specialized databases (IEDB, IMGT, SAbDab, OpenTargets, FAERS) with strict parameter formats and domain-specific reasoning. This Skill guides AI agents through verified immunology workflows so answers are grounded in database evidence rather than guesswork.

Core Features & Use Cases

  • Antibody and Epitope Analysis: Search SAbDab/TheraSAbDab for antibody structures and therapeutics, and query IEDB for T-cell/B-cell epitopes, MHC binding data, and TCR/BCR sequences.
  • Autoimmune Disease Genetics: Map diseases to genes via Orphanet and GWAS, then run pathway enrichment with KEGG and Reactome to build multi-layer evidence.
  • Immunotherapy Safety Profiling: Compute FAERS disproportionality signals (PRR, ROR, IC), compare drugs, and cross-check target safety via OpenTargets.
  • Use Case: To evaluate an immune checkpoint inhibitor, resolve its target with OpenTargets, pull co-crystal structures from SAbDab, check IEDB epitope data, and compare adverse event profiles against a competitor drug in FAERS.

Quick Start

Ask the agent to compare the adverse event profiles of pembrolizumab and nivolumab and summarize the target biology of PD-1 using immunology databases.

Frequently Asked Questions about tooluniverse-immunology

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

FAQPage Schema
How do I look up antibody structures and therapeutic antibodies?▼

Use SAbDab_get_structure with a PDB ID for structure and chain details, and TheraSAbDab_search_therapeutics with a drug name like pembrolizumab for INN, target, format, and clinical phase. Note that SAbDab_search_structures returns a browse URL, not JSON data.

How do I find T-cell epitopes and MHC binding data in IEDB?▼

Use iedb_search_epitopes with sequence_contains or structure_type filters, and iedb_search_tcell_assays with mhc_class and qualitative_measure parameters. Detail tools like iedb_get_epitope_mhc retrieve MHC data by structure_id.

Why does my IntAct interaction query return zero results?▼

IntAct requires a UniProt accession such as Q9NZQ7, not a gene symbol like CD274. Gene symbols return zero results, so resolve the protein to its UniProt accession first before calling intact_get_interaction_network.

Can I compare adverse events between two immunotherapy drugs?▼

Yes, use FAERS_compare_drugs with two generic drug names and an adverse event to get head-to-head disproportionality. Use generic names like pembrolizumab rather than brand names like Keytruda, and treat PRR signals as hypotheses, not causal proof.

What are the limitations of TIMER2 immune infiltration estimates?▼

TIMER2_immune_estimation returns computational deconvolution estimates for TCGA cancers, which are model-based approximations. The skill requires orthogonal validation with independent methods before drawing conclusions about tumor immune microenvironment composition.

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