"A database management system named MySQL" matching MCP servers:

MCP server for the STRING protein–protein interaction database, hosted by STRING at mcp.string-db.org. Adapted for LLM grounding: responses are size-limited and include metadata and notes on interpretation and next steps. Tools cover identifier resolution, interaction networks and evidence, functional and PPI enrichment, and sequence similarity search.

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.

An MCP server that grounds protein research in the UniProt SPARQL endpoint, providing tools for querying proteins, sequences, variants, diseases, and more via intent-named tools and raw SPARQL.

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.

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 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.

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.

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

Enables AI agents to search and retrieve compounds, drugs, diseases, pathways, genes, enzymes, glycans, modules, and KO entries; fetch full parsed flat-file entries by ID; and list database contents through keyless REST tools.

Enables AI agents to query the PomBase fission yeast model-organism database for genetic and molecular data through the Pipeworx MCP gateway.

Enables AI agents to resolve marine species names to OBIS taxon records, retrieve georeferenced ocean occurrence records with optional date filtering, and pull aggregate statistics such as record counts, contributing datasets, and observed year ranges. Queries the Ocean Biodiversity Information System keylessly over the Pipeworx gateway or as a local stdio server.

Enables querying roughly 3.2 million measured protein–ligand binding affinities from a local, read-only DuckDB build of the BindingDB MySQL dump, with tools for searching compounds and targets, retrieving potency and selectivity profiles, fetching activity records with assay and citation details, and running read-only SQL.

Enables users to look up yeast genes/loci, search genes and alleles by free text, and retrieve Gene Ontology annotations from the Saccharomyces Genome Database.

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 look up molecular interactions from the EBI IntAct database by gene/protein name or UniProt ID, returning detection method, interaction type, organism, PubMed reference, and MI confidence score, along with fast interaction counts. It is keyless and available either through a hosted MCP endpoint, a plain HTTP API, or a local stdio server.

Enables AI assistants to search and resolve taxon names, query divergence times between taxa, build evolutionary timelines for a taxon, and retrieve database metadata via MCP tools.

Enables querying the BOLD Systems global DNA barcode database for specimen records, taxonomy, barcode sequences, and BIN clusters, with keyless access and FASTA-ready output.

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.

Enables querying the CIViC database for clinical interpretations of cancer variants through tools like get_variant_evidence and get_variant_assertions.

Provides access to the AlphaFold Protein Structure Database with tools for structure retrieval, confidence analysis, batch processing, and visualization.

Manages local protein experiments with a Flask backend and SQLite, offering tools for protein library management, Beer-Lambert concentration calculations, BLI dilution planning, and experiment archiving. It provides 7 MCP tools for AI assistants like Claude to interact with the system.

Enables language models to search biomedical literature, fetch sequences, and follow links across Entrez databases through eleven read-only tools wrapping the nine NCBI Entrez E-utilities. It handles URL building, pacing, redirects, response caps, and API-key redaction so queries can be answered without a browser or scraping.