"Free tools or resources that do not require an API" matching MCP servers:

• 

  FLASK-toolsofficial

  FLASK-LLNL

  F

  license

  -

  quality

  B

  maintenance

  Provides a collection of MCP servers for computational chemistry tasks including molecular generation and retrosynthesis. Also offers property prediction and molecule pricing capabilities.

  Last updated 2026-07-31

• VEPmcp

  not-a-feature

  A

  license

  A

  quality

  C

  maintenance

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

  Last updated 2025-08-18

  9

  1

  MIT

• Evo2 MCP Server

  not-a-feature

  A

  license

  A

  quality

  C

  maintenance

  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 2026-04-13

  6

  2

  LGPL 3.0

• scvi-tools MCP Server

  hyennnnnnn

  A

  license

  -

  quality

  D

  maintenance

  Enables deep probabilistic analysis of single-cell omics data using scvi-tools through natural language. Supports SCVI for scRNA-seq analysis, SCANVI for cell type annotation, TOTALVI for multi-modal RNA/protein data, and PEAKVI for scATAC-seq analysis.

  Last updated 2025-10-14

  MIT

• MOF Tools MCP Server

  liuyuxiang92

  A

  license

  -

  quality

  D

  maintenance

  A specialized MCP server for Metal-Organic Framework research that provides tools for database searching, structural optimization, and energy calculations via ASE. It enables scientific workflows by allowing users to interact with MOF data and perform chemical simulations through a standard SSE interface.

  Last updated 2026-04-07

  MIT

• gget-cryo

  IrisApo13

  A

  license

  -

  quality

  C

  maintenance

  Enables searching cryo-EM density maps in EMDB and raw datasets in EMPIAR, with filtering by resolution, keyword, and cross-referencing between the two databases.

  Last updated 2026-06-18

  MIT

• 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
• 

  BioContextAI Knowledgebase MCPofficial

  biocontext-ai

  A

  license

  A

  quality

  C

  maintenance

  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

  28

  Apache 2.0

• kegg-mcp

  AriaShishegaran

  A

  license

  -

  quality

  B

  maintenance

  An MCP server that exposes the KEGG REST API — pathways, genes, compounds, reactions, enzymes, diseases, drugs, modules, orthology, glycans, and BRITE hierarchies, with cross-database linking. Provides 34 tools and 8 resource templates.

  Last updated 2026-07-06

  MIT

• genefoundry

  berntpopp

  A

  license

  -

  quality

  A

  maintenance

  Federates 13 gene-related MCP backends (gnomAD, GTEx, etc.) behind a single Streamable HTTP endpoint with collision-free namespacing and search-based tool discovery.

  Last updated 2026-08-01

  1

  MIT

• protein-design-mcp

  jasonkim8652

  A

  license

  -

  quality

  C

  maintenance

  An MCP server that gives LLM agents access to computational protein design tools.

  Last updated 2026-04-15

  14

  Apache 2.0

• TogoMCP

  arkinjo

  A

  license

  -

  quality

  F

  maintenance

  Executes SPARQL queries against biological and biomedical RDF databases from the RDF Portal, with additional REST API integrations for bioinformatics resources.

  Last updated 2025-12-16

  1

  MIT

• 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

• BioContextAI Knowledgebase MCP

  fastmcp-me

  A

  license

  -

  quality

  D

  maintenance

  A unified MCP server for biomedical research that connects AI systems to resources like Ensembl, EuropePMC, STRING, and more, enabling retrieval of verified domain-specific information.

  Last updated 2026-01-19

  Apache 2.0

• MARRVEL-MCP

  hyunhwan-bcm

  F

  license

  -

  quality

  C

  maintenance

  An MCP server for MARRVEL that enables AI agents to access genetics databases and variant analysis tools for rare disease research.

  Last updated 2026-04-01

  18

• OrigeneMCP

  GENTEL-lab

  F

  license

  -

  quality

  D

  maintenance

  An advanced integrated MCP server platform that combines 600+ tools and multiple biomedical databases to enable comprehensive information retrieval across molecules, proteins, genes, and diseases for accelerating therapeutic research.

  Last updated 2026-02-24

  37

• InterProScan MCP Service

  AltriaPendragon49

  F

  license

  -

  quality

  C

  maintenance

  Provides protein family, domain, and functional annotation using InterProScan, supporting local or API backends.

  Last updated 2026-06-30

• MGnify MCP Server

  MGS-sails

  F

  license

  -

  quality

  C

  maintenance

  Enables interaction with MGnify metagenomics resources and tools through the Model Context Protocol. Provides access to MGnify's API for querying and analyzing metagenomic datasets and related biological information.

  Last updated 2026-05-19

  1

• uniprot-link

  berntpopp

  A

  license

  A

  quality

  A

  maintenance

  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.

  Last updated 2026-08-05

  15

  MIT

• gencc-link

  berntpopp

  A

  license

  A

  quality

  A

  maintenance

  MCP server that provides tools to query harmonized gene-disease validity data from the Gene Curation Coalition, supporting consensus and conflict detection for gene-disease assertions.

  Last updated 2026-08-05

  12

  MIT