"A graph database management system: Neo4j" matching MCP servers:

Enables LLMs and AI agents to search a biomedical knowledge graph for concepts and study variables, traverse semantic relationships, and look up BioData Catalyst PIC-SURE paths for cohort building.

Enables LLMs and AI agents to query a biomedical knowledge graph stored in RedisGraph, with tools for concept search, synonym enrichment, and study variable discovery through semantic relationships.

Enables 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).

Enables variant annotation and effect prediction using the Ensembl VEP API, with support for batch and single queries.

Provides GPU-accelerated scientific computing capabilities including symbolic mathematics, quantum wave mechanics simulations, molecular dynamics, and neural network training through four specialized MCP servers.

Provides seamless access to UniProtKB protein database, enabling queries for protein entries, sequences, Gene Ontology annotations, full-text search, and ID mapping across 200+ database types.

A comprehensive Model Context Protocol (MCP) server that provides access to the AlphaFold Protein Structure Database through a rich set of tools and resources for protein structure prediction analysis.

A comprehensive Model Context Protocol (MCP) server providing advanced access to the ChEMBL chemical database.

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.

A comprehensive Model Context Protocol (MCP) server providing advanced access to the UniProt protein database.

Agent-callable canine genomics API providing breed-stratified allele frequencies, pathogenicity predictions, and variant-gene-breed-disease knowledge graph for dog DNA.

Enables querying the gnomAD genome aggregation database for variant, gene, and region information.

MCP server that exposes STRING database functionality, allowing AI agents to resolve protein identifiers, retrieve interaction networks, perform homology lookups, and run functional enrichment analysis.

Enables querying of the Monarch Initiative biomedical knowledge graph for genes, diseases, phenotypes, and their associations through natural language or direct tool calls.

Enables looking up genes, fetching sequences, predicting variant consequences, finding orthologs, and cross-database xrefs via Ensembl REST API through MCP.

Enables querying metadata from MyVariant.info, a comprehensive variant annotation database, providing dataset statistics, source information, and build versions.

Enables AI agents to query the WikiPathways open community pathway database via natural language, part of the Pipeworx MCP gateway.

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

A unified biomedical graph database that integrates 50+ primary data sources — genes, proteins, compounds, diseases, pathways, and clinical data — into a single queryable graph with billions of cross-reference edges. Its native MCP server gives LLMs direct access to structured, authoritative biomedical data, complementing their reasoning with reliable identifiers and up-to-date database content.

Enables querying celltype markers from CellMarker database using natural language.