ToolUniverse is a collection of tools, interfaces, and supporting components for building AI systems that perform scientific work. It is for developers creating AI scientist agents that use APIs, databases, machine-learning tools, and domain-specific utilities. The catalogue includes skills, commands, an MCP server, an agent, and a hook for working with the ecosystem.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add mims-harvard/ToolUniverse --skill tooluniverse-structural-proteomicsgit clone --depth 1 https://github.com/mims-harvard/ToolUniverseWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-structural-proteomics)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-structural-proteomics"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-structural-proteomics/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-structural-proteomics"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-structural-proteomics.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00186 | $0.07499 |
| Opus 5.5 | $0.00074 | $0.03000 |
| Sonnet 5.5 | $0.00037 | $0.01500 |
| Haiku 4.5 | $0.00019 | $0.00750 |
Grade A, and why
tooluniverse-structural-proteomics scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 10d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
- MobiDB: `MobiDB_get_protein` and `MobiDB_get_consensus` were verified live (repeatedly, with a 90s timeout) to hang indefinitely against their configured endpoint (`https://mobidb.org/api/download`) -- confirmed indepe How it starts
The opening of the file, as written. The whole thing — 318 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Structural Proteomics for Drug Target Validation
Comprehensive structural data integration using ToolUniverse tools across PDB, AlphaFold, GPCRdb, SAbDab, and proteomics databases for drug target validation.
LOOK UP DON'T GUESS
- PDB structures/resolutions:
PDBeSIFTS_get_best_structuresandRCSBGraphQL_get_structure_summary - AlphaFold confidence:
alphafold_get_summary - Ligands/affinities:
PDBe_get_structure_ligandsandBindingDB_get_ligands_by_uniprot - Protein-protein binding mutations (ddG):
SKEMPI_search_by_structure/SKEMPI_search_by_protein/SKEMPI_get_mutation-- BindingDB's protein-protein equivalent, for interface-mutation affinity effects rather than small-molecule ligands - Druggability:
ProteinsPlus_predict_binding_sites
COMPUTE, DON'T DESCRIBE
When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.
Domain Reasoning
Resolution determines valid conclusions: <2A = atom positions visible; 2-3A = side chains reliable, drug design supported; >3A = backbone only, binding site unreliable. Do not over-interpret low-resolution structures.
Tool Inventory
PDB (RCSB)
RCSBAdvSearch_search_structures (query_type, query_value, rows), RCSBData_get_entry (entry_id), RCSBGraphQL_get_structure_summary (pdb_id), RCSBGraphQL_get_ligand_info (pdb_id), RCSB_get_chemical_component (comp_id)
PDB (PDBe)
pdbe_get_entry_summary (pdb_id), PDBe_get_structure_ligands (pdb_id), PDBe_get_bound_molecules (pdb_id), PDBeSearch_search_structures (query, rows), PDBeSIFTS_get_best_structures (uniprot_id), PDBeSIFTS_get_all_structures (uniprot_id), PDBe_KB_get_ligand_sites (pdb_id), PDBe_KB_get_interface_residues (pdb_id), PDBeValidation_get_quality_scores (pdb_id)
PDBe PISA
PDBePISA_get_interfaces (pdb_id), PDBePISA_get_assemblies (pdb_id)
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 10d ago Changed · +179 lines · +96 tokens per session ad0efa6cf00d
- 1mo ago Changed · +1 lines 4b3a164161a6
- 1mo ago First seen · 138 lines · 90 tokens per session scan A 617542ae791b
tooluniverse-structural-proteomics is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,744 stars, last pushed yesterday), licensed Apache-2.0. It adds 186 tokens to every session and 7,499 once invoked, about $0.0007 per session on Opus 5.5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
Other skills, from other repositories
ai-agent-tool-routing
Use when designing or reviewing an AI agent tool registry or MCP router: document parameter schemas, caller authorization, execution limits, replay-safe retries and verification evidence.
nanoresearch-writing
Draft a LaTeX research paper from all previous stage outputs.
construct-toy-examples
Generate and analyze simpler examples that satisfy both the assumptions and the conclusion of a theorem statement or subgoal. Use when you are stuck in reasoning and need simpler examples to regain traction, or when you want to see where the assumptions take effect and gain intuition.
obtain-immediate-conclusions
Derive immediate mathematical consequences from a theorem statement or subgoal. Use when starting a new problem, branch, or subgoal, or when cheap progress or a cleaner reformulation is needed before deeper proof search.
clinical-research-analysis-framework
Guided workflow for statistical and ML analysis of clinical data. Use when planning or executing research analyses on MIMIC, eICU, or similar EHR data. Ensures methodological rigor through structured consultation, assumption checking, and stepwise execution with audit trails.
apache-iv-score
Calculate APACHE IV (Acute Physiology and Chronic Health Evaluation IV) score for ICU mortality prediction. Use for severity assessment, hospital mortality prediction, ICU benchmarking, or case-mix adjustment. eICU has pre-computed scores; MIMIC-IV requires custom implementation with diagnosis mapping challenges.