"Connect to MySQL server, edit database structure, and run manual migrations" matching MCP servers:

Searches UniProt by protein name to find accession numbers and retrieves detailed protein structure information from AlphaFold, including direct links to 3D structural predictions.

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.

Renders interactive 2D molecular structure diagrams from SMILES notation and computes molecular properties like molecular weight, LogP, and TPSA, directly in the chat.

Enables AI assistants to run reproducible bioinformatics pipelines over MCP, with verifiable provenance via checksums and Workflow Run RO-Crate metadata.

Enables MCP hosts to run provenance-aware computational epitope research workflows, including sequence and immune-evidence analysis, structure and chemistry calculations, molecular docking, and checksummed 3D artifact exports.

Run real bioinformatics from your AI agent on your own GPUs: MMseqs2 homology search, ESMFold structure prediction and sequence tools for Claude, Cursor and Codex. GPU-aware scheduling for shared machines, fail-fast input checks, background jobs, agent-friendly results and provenance for every run.

Enables natural language control of UCSF ChimeraX for protein structure visualization, editing, and analysis through MCP clients.

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 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.

Enables searching, retrieving, and downloading protein structure data from the RCSB Protein Data Bank. Supports intelligent protein structure search, comprehensive data retrieval, and multiple file format downloads for bioinformatics research.

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.

Provides comprehensive BioPython capabilities for biological sequence analysis, alignment, database access (GenBank, UniProt, PubMed), protein structure analysis, and phylogenetics through a Model Context Protocol interface for AI-assisted bioinformatics workflows.

Enables protein structure and sequence searches using FoldSeek, with support for multiple databases, automatic model downloads, and structured job management.

Provides programmatic access to AlphaFold protein structure predictions and UniProt data, enabling users to retrieve protein structures, summaries, and annotations through natural language.

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

Enables comprehensive access to PubChem's chemical database with over 110 million compounds. Supports chemical searches, structure analysis, bioactivity data, safety information, and molecular property calculations through 30 specialized tools.

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.

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

A Model Context Protocol server that lets you drive PyMOL with natural language, enabling structure loading, analytical views, measurements, and protein exploration through AI assistants.

Enables AI assistants to perform NCBI BLAST sequence similarity searches through natural language, supporting nucleotide and protein searches, custom database creation, and multiple output formats.

Bridge any AI coding assistant directly to GenePattern — run bioinformatics modules, manage cloud jobs, and stream results, all through natural language.

MCP server for interacting with Galaxy bioinformatics platform, enabling AI assistants to connect to Galaxy instances, search and execute tools, manage workflows, and access other features.

Enables querying gene expression experiments, brain region structure ontologies, and in-situ hybridization datasets from the Allen Institute's Brain Atlas public API.

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

Enables AI clients to connect to Galaxy instances, inspect histories and reports, discover tools and workflows, submit analyses, and monitor their results via interactive cards.

Enables AI agents to control RELION 5.x cryo-EM structure determination software through natural language, providing 23 tools for the complete single-particle analysis pipeline.

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 searching a manually curated database of stable macromolecular protein complexes by protein or complex name, gene, GO term, or biological process, and fetching individual records by accession to retrieve subunits with UniProt identifiers, biological roles, and stoichiometry. Complements UniProt, IntAct, and STRING, and can be used keyless over a hosted gateway endpoint or run locally over stdio.

Exposes pipen bioinformatics pipelines as MCP tools, allowing AI assistants to discover and run complex workflows through a progressive disclosure interface.

Dog-specific aging tools: HAGR dog rows (AnAge/DrugAge/GenAge), dog orthologs of aging genes via Ensembl, FDA Km dose translation, Dog Aging Project codebooks, NIH RePORTER grants, BM25 search over 3,500+ canine aging papers, FDA CVM FOI summaries with quote-grounded PK and safety data, and an intervention dossier that composes them. Installs with uvx; downloads its database on first run.