An MCP server that provides standardized access to biomedical knowledge bases and resources, enabling AI systems to retrieve verified information from sources like bioRxiv, EuropePMC, and various protein/gene databases.

AlphaFold MCP Server

A comprehensive Model Context Protocol (MCP) server for accessing the STRING protein interaction database. This server provides powerful tools for protein network analysis, functional enrichment, and comparative genomics through the STRING API.

An MCP server that enables single-cell RNA sequencing analysis through natural language, supporting data processing, visualization, and analysis tasks without requiring coding knowledge.

A Model Context Protocol server that interfaces with Biomart databases, allowing models to discover biological datasets, explore attributes/filters, retrieve biological data, and translate between different biological identifiers.

Provides LLMs with structured access to critical biomedical databases including PubTator3 (PubMed/PMC), ClinicalTrials.gov, and MyVariant.info through the Model Context Protocol.

A comprehensive Model Context Protocol server providing access to over 110 million chemical compounds with extensive molecular properties, bioassay data, and chemical informatics tools from the PubChem database.

Search PubMed for articles matching the query.

UniProt MCP Server

ChEMBL MCP Server

A Model Context Protocol server providing LLMs with access to the Ensembl genomics database, enabling AI assistants to query gene information, sequences, variants, and other genomic data across multiple species.

A bridge connecting AI agents to NCBI's PubMed database through the Model Context Protocol, enabling seamless searching, retrieval, and analysis of biomedical literature and data.

PDB MCP Server

A server that enables AI assistants to interact with cancer genomics data from cBioPortal, allowing users to explore cancer studies, access genomic data, and retrieve mutations and clinical information.

Enables AI assistants to access protein information directly from UniProt, allowing retrieval of protein names, functions, sequences, and organism data by accession number.

Provides standardized access to aging and longevity research data from the OpenGenes database, enabling AI assistants to query comprehensive biomedical datasets through SQL and structured interfaces.

A production-ready Model Context Protocol (MCP) server that provides comprehensive access to the BioOntology API for searching, annotating, and exploring over 1,200 biological ontologies.

A Model Context Protocol server that enhances language models with protein structure analysis capabilities, enabling detailed active site analysis and disease-related protein searches through established protein databases.

Leverages large language models to analyze users' WeGene genetic testing reports, providing access to report data via custom URI schemes and enabling profile and report management through OAuth authentication and API utilization.

Connects 3D Slicer with AI assistants through the Model Context Protocol, enabling medical image processing and scene manipulation using natural language.

Enables users to manage and navigate nf-core bioinformatics pipeline repositories, allowing list, search, and explore operations on pipeline configurations, workflows, and modules.

An MCP server that enables language models to fetch protein information from the UniProt database, including protein details, sequences, functions, and structures.

A Model Context Protocol server that enables AI assistants to interact with LAMMPS for molecular dynamics simulations through natural language commands.

🔍 Enable AI assistants to search, access, and analyze PubMed articles through a simple MCP interface.

Connects PyMOL to Claude AI through the Model Context Protocol, allowing for conversational structural biology and molecular visualization through natural language commands.

Server to search PubMed (PubMed is a free, online database that allows users to search for biomedical and life sciences literature). I have created on a day MCP came out but was on vacation, I saw someone post similar server in your DB, but figured to post mine.

🔍 A biomedical literature annotation and relationship mining server based on PubTator3, providing convenient access through the MCP interface.

Provides access to the ClinicalTrials.gov AACT database, enabling analysis of clinical trial data, tracking development trends, and generating therapeutic landscape insights.

A Model Context Protocol server that enables AI models to programmatically search and interact with proteomics datasets from the PRIDE Archive repository through structured function calling.

Enables search and retrieval of academic papers from PubMed database with advanced features like MeSH term lookup, publication statistics, and PICO-based evidence search.

A Model Control Protocol implementation for SAMtools, providing a standardized interface for working with SAM/BAM/CRAM files.

This server enables multi-agent conversations for interacting with Cirro's biological data platform through its OpenAPI interface, auto-generated using AG2's MCP builder.

🔍 Enable AI assistants to search and access bioRxiv papers through a simple MCP interface. The bioRxiv MCP Server provides a bridge between AI assistants and bioRxiv's preprint repository through the Model Context Protocol (MCP). It allows AI models to search for biology preprints and access their

A framework that integrates Brain-Computer Interface technology with the Model Context Protocol to enable real-time neural signal processing and AI-powered interactions for healthcare, accessibility, and research applications.