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maintenanceProvides an MCP interface to the ROBOT command-line tool for OWL ontology editing, enabling operations like merging, reasoning, and conversion via natural language.
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BSD 2-Clause "Simplified"
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"A tool to manage and process a list of Swagger API endpoints" matching MCP servers:
- AlicenseAqualityCmaintenanceEnables genomic sequence analysis through the Evo 2 model, supporting DNA sequence scoring, embedding, generation, and variant effect prediction with multiple model checkpoints (7B, 40B, 1B parameters).62LGPL 3.0
- AlicenseAqualityCmaintenanceEnables variant annotation and effect prediction using the Ensembl VEP API, with support for batch and single queries.91MIT
- FlicenseAqualityDmaintenanceProvides access to EMBL-EBI bioinformatics data including InterPro domains, Pfam families, protein features, and taxonomy through a unified tool.11
- AlicenseAqualityAmaintenanceA stateless, deterministic Bio-Robotics Core Engine converting biological data (UniProt API) to G-code.6MIT
- AlicenseBqualityDmaintenanceEnables AI-powered genomic variant analysis including variant impact prediction, regulatory element discovery, and batch variant scoring. Currently operates in mock mode as a proof-of-concept awaiting the public release of Google DeepMind's AlphaGenome API.20142MIT
- AlicenseBqualityDmaintenanceProvides seamless access to UniProtKB protein data, enabling querying of protein entries, sequences, Gene Ontology annotations, and ID mappings through a typed, resilient interface.5MIT
NGS360 MCP Serverofficial
FlicenseCqualityBmaintenanceExposes the NGS360 bioinformatics platform REST API as MCP tools, enabling AI assistants to manage sequencing runs, projects, workflows, and more through natural language.82- FlicenseDqualityDmaintenanceEnables users to manage and navigate nf-core bioinformatics pipeline repositories, allowing list, search, and explore operations on pipeline configurations, workflows, and modules.3
- Alicense-qualityDmaintenanceA Model Context Protocol server that enables retrieval of -omics data from sources like PDB, ChEMBL, UniProt, PubChem, and HUGO.5GPL 3.0
- Alicense-qualityCmaintenanceMCP server for querying the GWAS Catalog (EBI/NHGRI), a curated catalog of genome-wide association studies. It enables AI agents to search and retrieve study data via natural language or direct tool calls.4MIT
- Alicense-qualityCmaintenanceEnables querying of the Monarch Initiative biomedical knowledge graph for genes, diseases, phenotypes, and their associations through natural language or direct tool calls.10MIT
OpenCRAVATofficial
Flicense-qualityCmaintenanceAnnotate variants by with a deep and rich set of data. Can annotate: genetic change, rsID, CAid, HGVS (g./c./p.), protein change.5- Alicense-qualityAmaintenanceFederates 13 gene-related MCP backends (gnomAD, GTEx, etc.) behind a single Streamable HTTP endpoint with collision-free namespacing and search-based tool discovery.2MIT
- Alicense-qualityAmaintenanceA Model Context Protocol server providing programmatic access to 3D protein structural data from RCSB PDB, PDBe, and UniProt, enabling search, retrieval, comparison, and analysis of protein structures.1285Apache 2.0
- Alicense-qualityAmaintenanceA collaborative BrAPI v2.1 workspace for multi-agent research via MCP, enabling search and retrieval of studies, germplasm, genotypes, and more across any BrAPI v2-compliant server.3403Apache 2.0
- Alicense-qualityDmaintenanceValidates the physical and chemical plausibility of ligand–protein docking poses using the PoseBusters tool.5BSD 3-Clause
- Alicense-qualityDmaintenanceProvides MCP tool adapters for Bioconductor methods like limma, DESeq2, and fgsea, enabling statistical analysis of omics data through containerized R execution. It serves as a bridge between MCP clients and bioinformatics tools for reproducible research workflows.Apache 2.0
- Alicense-qualityDmaintenanceProvides chemical informatics endpoints for converting between chemical names and SMILES, processing molecule structures, and comparing molecules, with MCP compatibility.4MIT
FLASK-toolsofficial
Flicense-qualityBmaintenanceProvides a collection of MCP servers for computational chemistry tasks including molecular generation and retrosynthesis. Also offers property prediction and molecule pricing capabilities.
