"Gathering Context from an Ubuntu Server" matching MCP servers:

• protein-mcp-server

  cyanheads

  A

  license

  -

  quality

  A

  maintenance

  A Model Context Protocol server providing programmatic access to 3D protein structural data from RCSB PDB, PDBe, and UniProt, enabling search, retrieval, comparison, and analysis of protein structures.

  Last updated 2026-07-03

  212

  5

  Apache 2.0

• UniProt MCP Server

  vitamin3615

  A

  license

  -

  quality

  D

  maintenance

  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

• clinicaltrialsgov-mcp-server

  cyanheads

  A

  license

  A

  quality

  A

  maintenance

  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 2026-07-09

  7

  1,393

  81

  Apache 2.0

• pubmed-mcp-server

  cyanheads

  A

  license

  A

  quality

  A

  maintenance

  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 2026-06-30

  10

  2,427

  121

  Apache 2.0

• Gen3 MCP Server

  delocalizer

  A

  license

  A

  quality

  D

  maintenance

  A Model Context Protocol (MCP) server for interacting with Gen3 data commons, with GraphQL query validation to reduce hallucinations.

  Last updated 2025-06-13

  5

  4

  MIT

• pubchem-mcp-server

  cyanheads

  A

  license

  A

  quality

  A

  maintenance

  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 2026-07-03

  10

  944

  9

  Apache 2.0

• Rosetta MCP Server

  Arielbs

  A

  license

  A

  quality

  F

  maintenance

  An MCP server that enables AI coding assistants to interact with Rosetta, PyRosetta, and Biotite for running RosettaScripts, validating XML, translating between Rosetta and Biotite, scoring structures, and querying documentation.

  Last updated 2026-04-05

  19

  238

  16

  MIT

• ncbi-datasets-mcp

  syntheticgio

  F

  license

  A

  quality

  A

  maintenance

  An MCP server that gives Claude access to NCBI Datasets v2 — search genome assembly metadata, retrieve taxonomy records, and download data packages without leaving your conversation.

  Last updated 2026-06-22

  10

• uniprot-unipressed-mcp

  pansapiens

  A

  license

  A

  quality

  D

  maintenance

  An MCP server that provides tools for searching and fetching protein data from the UniProt database using the unipressed library.

  Last updated 2026-01-21

  2

  MIT

• biothings-mcp

  longevity-genie

  A

  license

  A

  quality

  F

  maintenance

  Provides a Model Context Protocol server for accessing and querying biomedical data from BioThings services, including gene, variant, chemical, and taxon annotations.

  Last updated 2025-11-03

  19

  33

  MIT

• Enrichr MCP Server

  tianqitang1

  A

  license

  A

  quality

  B

  maintenance

  Enables gene set enrichment analysis using the Enrichr API across hundreds of gene set libraries including Gene Ontology, pathways, diseases, tissues, drugs, and transcription factors. Returns only statistically significant results for interpretation.

  Last updated 2026-07-14

  2

  357

  15

  MIT

• Ensembl MCP Server

  effieklimi

  A

  license

  A

  quality

  D

  maintenance

  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

  8

  JavaScript

  MIT

• BCI-MCP Server

  enkhbold470

  A

  license

  A

  quality

  C

  maintenance

  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.

  Last updated 2026-07-23

  12

  13

  MIT

• PDB MCP Server

  Augmented-Nature

  F

  license

  A

  quality

  F

  maintenance

  PDB MCP Server

  Last updated 2025-12-21

  5

  25

• OpenGenes MCP Server

  longevity-genie

  A

  license

  B

  quality

  F

  maintenance

  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

  20

  MIT

• Protein MCP Server

  gqy20

  A

  license

  B

  quality

  D

  maintenance

  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

• BioPython MCP Server

  kmaneesh

  A

  license

  B

  quality

  C

  maintenance

  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

• AGR MCP Server

  nuin

  A

  license

  B

  quality

  C

  maintenance

  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 2026-06-27

  22

  22

  MIT

• BioOntology MCP Server

  Augmented-Nature

  F

  license

  B

  quality

  D

  maintenance

  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.

  Last updated 2025-12-21

  10

  9

• AlphaFold MCP Server

  Augmented-Nature

  F

  license

  B

  quality

  F

  maintenance

  AlphaFold MCP Server

  Last updated 2025-12-21

  19

  35