smithery/mims-harvard

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setup-tooluniverse Install and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 9 subcommands),…

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tooluniverse ToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run r…

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tooluniverse-binder-discovery Discover novel small-molecule binders for protein targets using structure-based and ligand-based screening.

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tooluniverse-chemical-compound-retrieval Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry h…

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tooluniverse-disease-research Generate comprehensive disease research reports covering genetics (causal genes, GWAS, OMIM), pathways (Reactome, KEG…

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tooluniverse-drug-repurposing Identify drug repurposing candidates via target-based, compound-based, and disease-based strategies.

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tooluniverse-drug-research Comprehensive drug profiling — mechanism, primary/secondary targets, drug interactions, clinical-trial status, advers…

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tooluniverse-expression-data-retrieval Retrieve gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation and quality ass…

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tooluniverse-infectious-disease Rapid pathogen characterization and drug repurposing for outbreaks.

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tooluniverse-literature-deep-research Deep literature review — PubMed, EuropePMC, bioRxiv preprints, citation networks, evidence synthesis.

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tooluniverse-pharmacovigilance Drug safety and adverse event analysis — FAERS spontaneous-report mining, FDA black-box warnings, signal detection (P…

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tooluniverse-precision-oncology Cancer treatment recommendations from molecular profile (mutations + cancer type + biomarkers) — FDA-approved + inves…

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tooluniverse-protein-structure-retrieval Protein structure retrieval from RCSB PDB, PDBe, and AlphaFold with disambiguation, quality assessment (resolution, R…

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tooluniverse-protein-therapeutic-design AI-guided de novo protein design — RFdiffusion backbone generation, ProteinMPNN sequence design, structure validation…

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tooluniverse-rare-disease-diagnosis Rare disease differential diagnosis from patient phenotype — HPO term matching to candidate diseases (Orphanet, OMIM)…

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tooluniverse-sdk Build AI scientist systems with the ToolUniverse Python SDK for scientific research.

smithery/mims-harvard

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tooluniverse-sequence-retrieval Retrieve DNA/RNA/protein sequences from NCBI and ENA with disambiguation.

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tooluniverse-target-research Comprehensive drug-target intelligence — tissue expression (GTEx, HPA), pathways, protein interactions (STRING), vari…

smithery/mims-harvard

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