Popular MCP Servers

• 

  BioContextAI Knowledgebase MCPofficial

  biocontext-ai

  A

  security

  A

  license

  -

  quality

  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.

  Last updated 2026-01-12

  52

  22

  Apache 2.0
• 

  Noctua MCP Serverofficial

  geneontology

  A

  security

  A

  license

  -

  quality

  Enables editing and querying of Gene Ontology Causal Activity Models (GO-CAMs) through the Barista API. Supports model creation, individual and fact management, evidence addition, and causal pathway construction for biological knowledge representation.

  Last updated 2025-11-01

  18

  BSD 3-Clause
• 

  WormBase MCP Serverofficial

  WormBase

  A

  security

  A

  license

  -

  quality

  Enables querying the WormBase database for C. elegans and nematode genomics data, including gene information, protein sequences, phenotypes, interactions, and expression patterns through natural language.

  Last updated 2025-12-12

  12

  2

  MIT

• pubmed-mcp-server

  cyanheads

  A

  security

  A

  license

  -

  quality

  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.

  Last updated 2026-04-09

  1

  9

  2,208

  72

  Apache 2.0

• MCP Sequence Simulation Server

  coreymhudson

  A

  security

  A

  license

  -

  quality

  Enables the generation, mutation, and evolution of DNA and protein sequences using various evolutionary models and phylogenetic algorithms. It supports realistic next-generation sequencing read simulation and population-level evolutionary tracking for bioinformatics research and testing.

  Last updated 2025-06-17

  6

  BSD 2-Clause "Simplified"

• AlphaGenome MCP Server

  taehojo

  A

  security

  A

  license

  -

  quality

  Enables 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.

  Last updated 2026-03-03

  20

  4

  2

  MIT

• Bio-OS MCP Server

  GBA-BI

  A

  security

  A

  license

  -

  quality

  Enables workflow management and Docker image building for Bio-OS platform. Supports WDL workflow submission, validation, and monitoring, along with Docker image building and status tracking for bioinformatics workflows.

  Last updated 2026-03-11

  22

  4

  MIT

• genome-mcp

  gqy20

  A

  security

  A

  license

  -

  quality

  Intelligent Genomic Data Server Provides high-quality gene information queries, homologous gene analysis, and evolutionary research functions via the MCP protocol.

  Last updated 2025-12-08

  6

  2

  MIT

• BioPython MCP Server

  kmaneesh

  A

  security

  A

  license

  -

  quality

  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.

  Last updated 2026-01-16

  32

  2

  MIT

• Biomart MCP

  jzinno

  A

  security

  A

  license

  -

  quality

  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.

  Last updated 2025-05-21

  8

  7

  MIT

• UniProt MCP Server

  TakumiY235

  A

  security

  A

  license

  -

  quality

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

  Last updated 2025-03-11

  2

  11

  MIT

• clinicaltrialsgov-mcp-server

  cyanheads

  A

  security

  A

  license

  -

  quality

  Empowers AI agents with direct access to the official ClinicalTrials.gov database, enabling programmatic searching, retrieval, and analysis of clinical study data through a Model Context Protocol interface.

  Last updated 2026-04-06

  7

  1,346

  64

  Apache 2.0

• pubchem-mcp-server

  cyanheads

  A

  security

  A

  license

  -

  quality

  Enables AI agents and applications to search, retrieve, and analyze chemical compounds, substances, and bioassays from PubChem's vast chemical information database through comprehensive tools for chemical research and discovery.

  Last updated 2026-03-30

  8

  75

  8

  Apache 2.0

• Protein MCP Server

  gqy20

  A

  security

  A

  license

  -

  quality

  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.

  Last updated 2025-10-24

  3

  MIT

• SCMCP

  huang-sh

  A

  security

  A

  license

  -

  quality

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

  Last updated 2025-05-15

  52

  12

  BSD 3-Clause

• cBioPortal MCP Server

  pickleton89

  A

  security

  A

  license

  -

  quality

  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.

  Last updated 2025-07-21

  17

  5

  MIT

• BioMCP

  genomoncology

  A

  security

  A

  license

  -

  quality

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

  Last updated 2026-04-11

  35

  484

  MIT

• PubChem MCP Server

  k-lordbodin7

  A

  security

  A

  license

  -

  quality

  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.

  Last updated 2025-09-29

  30

  MIT

• STRING MCP Server

  munch-group

  A

  security

  A

  license

  -

  quality

  Provides access to the STRING protein-protein interaction database for mapping identifiers, retrieving interaction networks, and performing functional enrichment analysis. It enables users to explore protein partners, pathways, and cross-species homology through natural language interactions.

  Last updated 2025-12-09

  9

  ISC

• encode-toolkit

  ammawla

  A

  security

  A

  license

  -

  quality

  MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments

  Last updated 2026-03-29

  20

  32

  4

  AGPL 3.0

• OpenGenes MCP Server

  longevity-genie

  A

  security

  A

  license

  -

  quality

  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.

  Last updated 2025-10-14

  3

  17

  MIT

• UniProt MCP Server

  josefdc

  A

  security

  A

  license

  -

  quality

  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.

  Last updated 2026-03-02

  5

  2

  MIT

• UCSC Genome Browser MCP Server

  hlydecker

  A

  security

  A

  license

  -

  quality

  Provides comprehensive access to the UCSC Genome Browser API, enabling queries of genomic data, DNA sequences, gene annotations, variants, and metadata across multiple species and assemblies.

  Last updated 2025-11-13

  12

  2

  MIT

• ChatSpatial

  cafferychen777

  A

  security

  A

  license

  -

  quality

  Natural language-driven spatial transcriptomics analysis via MCP. Integrates 60+ methods for preprocessing, visualization, spatial statistics, cell communication, deconvolution, and trajectory analysis.

  Last updated 2026-04-04

  27

  MIT

• Ensembl MCP Server

  munch-group

  A

  security

  A

  license

  -

  quality

  Provides access to the Ensembl genomics REST API with 30+ tools for genomic data including gene lookup, sequence retrieval, genetic variants, cross-species homology, phenotypes, and regulatory features.

  Last updated 2025-12-09

  25

  ISC

• Ensembl MCP Server

  effieklimi

  A

  security

  A

  license

  -

  quality

  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.

  Last updated 2026-02-11

  10

  6

  JavaScript

  MIT

• pubmed-mcp-server

  AIAnytime

  A

  security

  A

  license

  -

  quality

  Search PubMed for articles matching the query.

  Last updated 2026-04-04

  1

  62

  MIT

• MCP PubMed Search

  wavelovey

  A

  security

  A

  license

  -

  quality

  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.

  Last updated 2024-12-12

  1

  47

  MIT

• Unofficial PubChem MCP Server

  Augmented-Nature

  A

  security

  F

  license

  -

  quality

  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.

  Last updated 2025-12-21

  2,872

  30

  36

• gnomAD MCP Server

  koido

  A

  security

  A

  license

  -

  quality

  Provides a programmatic interface to the Genome Aggregation Database (gnomAD) API across versions v2.1.1, v3.1.2, and v4.1.0. It enables users to query gene metadata, variant information, population frequencies, and ClinVar data through a unified schema.

  Last updated 2026-01-23

  12

  5

  Apache 2.0

• STRING-MCP

  MCPmed

  A

  security

  A

  license

  -

  quality

  A Model Context Protocol server that provides tools for interacting with the STRING database to analyze protein-protein interaction networks and functional enrichment. It enables users to map protein identifiers, retrieve interaction data, and generate biological network visualizations through natural language interfaces.

  Last updated 2025-07-28

  11

  3

  BSD 3-Clause

• Omics AI MCP Server

  mfiume

  A

  security

  A

  license

  -

  quality

  Enables AI agents to conversationally interact with genomics research networks for data analysis and discovery across multiple Omics AI Explorer platforms. It provides tools for exploring data collections, examining table schemas, and executing SQL queries against datasets like Viral AI and Neuroscience AI.

  Last updated 2025-06-20

  6

  MIT

• MolMIM MCP Server

  siarhei-fedziukovich

  -

  security

  A

  license

  -

  quality

  Enables molecular generation, optimization, and analysis through NVIDIA MolMIM API. Supports generating drug-like molecules with desired properties, extracting molecular embeddings, and exploring chemical space around seed molecules.

  Last updated 2025-08-26

  MIT

• ChEMBL MCP Server

  Augmented-Nature

  A

  security

  F

  license

  -

  quality

  ChEMBL MCP Server

  Last updated 2025-12-21

  27

  83

• miEAA3 MCP Server

  kkShrihari

  A

  security

  F

  license

  -

  quality

  Integrates the miEAA 3.x bioinformatics platform with Claude Desktop, enabling microRNA enrichment analysis, identifier conversion between miRBase versions, and miRNA-precursor transformations through natural language.

  Last updated 2025-12-19

  4
• 

  Bio-MCP BLASTofficial

  bio-mcp

  -

  security

  F

  license

  -

  quality

  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.

  Last updated 2025-06-29

  8

• BioMCP

  acashmoney

  A

  security

  F

  license

  -

  quality

  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.

  Last updated 2025-03-11

  2

  18

• Math-Physics-ML MCP System

  andylbrummer

  -

  security

  A

  license

  -

  quality

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

  Last updated 2026-02-08

  1

  MIT

• Poiesis MCP Server

  JaeAeich

  -

  security

  A

  license

  -

  quality

  Enables AI assistants to create, monitor, and manage computational tasks through GA4GH Task Execution Service (TES) functionality. Provides seamless access to TES-compliant services for executing bioinformatics and scientific computing workflows.

  Last updated 2025-09-25

  Apache 2.0

• AGR MCP Server

  nuin

  A

  security

  F

  license

  -

  quality

  Enables querying genomics data from the Alliance of Genome Resources across model organisms including human, mouse, rat, zebrafish, fly, worm, yeast, and xenopus. Supports gene searches, disease associations, expression data, orthologs, phenotypes, and molecular interactions through natural language.

  Last updated 2026-02-01

  22

  5

• UniProt MCP Server

  vitamin3615

  -

  security

  A

  license

  -

  quality

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

  Last updated 2025-04-01

  MIT

• Oh My KEGG MCP

  martinuslee

  -

  security

  A

  license

  -

  quality

  An MCP server that provides access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, offering 30 tools for searching and analyzing biological data like pathways, genes, and compounds. It supports integration with LangChain and Ollama to enable LLMs to interact with comprehensive genomic and chemical datasets.

  Last updated 2026-02-05

  8

  MIT

• PubMed-MCP-Server

  JackKuo666

  -

  security

  A

  license

  -

  quality

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

  Last updated 2025-05-08

  106

  MIT

• SCMCP

  scmcphub

  -

  security

  A

  license

  -

  quality

  An MCP server that enables scRNA-Seq analysis through natural language, providing tools for data preprocessing, clustering, and biological visualization. It supports both predefined function execution and a flexible code mode powered by a Jupyter backend for automated single-cell transcriptomics workflows.

  Last updated 2025-07-10

  15

  BSD 3-Clause

• AlphaFold MCP Server

  Augmented-Nature

  A

  security

  F

  license

  -

  quality

  AlphaFold MCP Server

  Last updated 2025-12-21

  19

  33

• gnomAD MCP Server

  shukwong

  A

  security

  F

  license

  -

  quality

  Enables AI assistants to query genetic variant data, gene constraints, and population genetics information from the gnomAD (Genome Aggregation Database) through its GraphQL API. Supports searching for genes and variants, retrieving constraint scores, analyzing population frequencies, and accessing genomic coverage data.

  Last updated 2025-08-13

  9

  10

• PDB MCP Server

  Augmented-Nature

  A

  security

  F

  license

  -

  quality

  PDB MCP Server

  Last updated 2025-12-21

  5

  24

• OneKGPd

  dnaerys

  -

  security

  A

  license

  -

  quality

  Access to 1000 Genomes Project dataset, hosted online in Dnaerys variant store

  Last updated 2026-04-06

  Apache 2.0

• GTEx MCP Server

  Augmented-Nature

  A

  security

  F

  license

  -

  quality

  Enables AI assistants to query and analyze genomics data from the GTEx Portal through 25 specialized tools for gene expression analysis, eQTL/sQTL associations, and genetic variant lookups across 54 human tissue types.

  Last updated 2025-12-21

  25

  2

• Evo2 MCP Server

  not-a-feature

  -

  security

  A

  license

  -

  quality

  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).

  Last updated 2025-11-11

  1

  LGPL 3.0