Molecular Biology MCP MCP Servers
MCP servers for querying and analyzing biological and chemical databases (PDB, UniProt, ChEMBL, PubChem), protein structures, molecular properties, and computational chemistry/toxicology workflows. Does NOT include general bioinformatics analysis tools, sequence alignment, or non-database-backed prediction services unrelated to molecular structure and chemical data.
There are 45 molecular biology mcp servers tracked. 2 score above 50 (established tier). The highest-rated is nickzren/opentargets-mcp at 56/100 with 15 stars and 230 monthly downloads.
Get all 45 projects as JSON
curl "https://pt-edge.onrender.com/api/v1/datasets/quality?domain=mcp&subcategory=molecular-biology-mcp&limit=20"
Open to everyone — 100 requests/day, no key needed. Get a free key for 1,000/day.
| # | Server | Score | Tier |
|---|---|---|---|
| 1 |
nickzren/opentargets-mcp
MCP server for Open Targets Data |
|
Established |
| 2 |
genomoncology/biomcp
BioMCP: Biomedical Model Context Protocol |
|
Established |
| 3 |
josefdc/Uniprot-MCP
UniProt MCP Server - Access comprehensive protein data via Model Context... |
|
Emerging |
| 4 |
biocontext-ai/registry
The BioContextAI Registry for biomedical MCP servers |
|
Emerging |
| 5 |
biocontext-ai/knowledgebase-mcp
BioContextAI Knowledgebase MCP server for biomedical agentic AI |
|
Emerging |
| 6 |
Augmented-Nature/ChEMBL-MCP-Server
A comprehensive Model Context Protocol (MCP) server providing advanced... |
|
Emerging |
| 7 |
tandemai-inc/rdkit-mcp-server
MCP server that enables language models to interact with RDKit through... |
|
Emerging |
| 8 |
Augmented-Nature/PubChem-MCP-Server
A comprehensive Model Context Protocol (MCP) server for accessing the... |
|
Emerging |
| 9 |
longevity-genie/biothings-mcp
MCP (Model Context Protocol) server for biothings |
|
Emerging |
| 10 |
cyanheads/pubchem-mcp-server
A Model Context Protocol (MCP) server providing comprehensive LLM tools for... |
|
Emerging |
| 11 |
Augmented-Nature/PDB-MCP-Server
A Model Context Protocol (MCP) server that provides access to the Protein... |
|
Emerging |
| 12 |
Augmented-Nature/Augmented-Nature-UniProt-MCP-Server
A comprehensive Model Context Protocol (MCP) server providing advanced... |
|
Emerging |
| 13 |
EBISPOT/GrEBI
HPC aggregation pipeline and API/MCP server for LLM-mediated biomedical data... |
|
Emerging |
| 14 |
spyrosze/mcp-openfoodtox
MCP server providing tools to access EFSA's comprehensive OpenFoodTox... |
|
Emerging |
| 15 |
Augmented-Nature/SureChEMBL-MCP-Server
A comprehensive Model Context Protocol (MCP) server for accessing the... |
|
Emerging |
| 16 |
sebotic/cdk_pywrapper
A Python wrapper for the Chemistry Development Kit (CDK) |
|
Emerging |
| 17 |
ToxMCP/admetlab-mcp
MCP server for ADMETlab 3.0 (washing, ADMET prediction, rendering, CSV retrieval). |
|
Emerging |
| 18 |
ToxMCP/pbpk-mcp
MCP server for PBPK modeling workflows (simulation control + PK analytics). |
|
Emerging |
| 19 |
cyanheads/protein-mcp-server
MCP Server for 3D protein structural data retrieval & analysis from RCSB... |
|
Emerging |
| 20 |
PabloPauling/posebusters-mcp-server
Unofficial MCP server for PoseBusters – validate molecular poses via HTTP or... |
|
Experimental |
| 21 |
hlydecker/ucsc-genome-mcp
An MCP server to interact with the UCSC Genome Browser API |
|
Experimental |
| 22 |
berntpopp/genefoundry
A modular registry for trustworthy, evidence-based genomic analysis powered... |
|
Experimental |
| 23 |
tom832/chemdraw-server
This repository provides a unified FastAPI and MCP wrapper for an API that... |
|
Experimental |
| 24 |
sakkkysaka/mcp-openfoodtox
🧪 Access EFSA's OpenFoodTox database for chemical hazards with a simple... |
|
Experimental |
| 25 |
genepattern/genepattern-mcp
MCP server that lets AI assistants (Claude, Cursor, Copilot) run GenePattern... |
|
Experimental |
| 26 |
borjanebbal/genomics-mcp
MCP server for genomics SNP trait lookup |
|
Experimental |
| 27 |
Genealogy-MCP/gramps-mcp
MCP server for Gramps Web — search, browse, and manage your genealogy... |
|
Experimental |
| 28 |
Genealogy-MCP/gedcom-mcp
MCP server for GEDCOM files — load, search, and explore your family tree... |
|
Experimental |
| 29 |
Genealogy-MCP/wikitree-mcp
MCP server for the WikiTree API — search profiles, explore ancestors and... |
|
Experimental |
| 30 |
Genealogy-MCP/familysearch-mcp
MCP server for the FamilySearch API — search places, standardize dates,... |
|
Experimental |
| 31 |
ToxMCP/aop-mcp
MCP server for Adverse Outcome Pathway (AOP) discovery, semantics, and draft... |
|
Experimental |
| 32 |
nickzren/monarch-mcp
MCP server for Monarch Initiative Data |
|
Experimental |
| 33 |
nickzren/mygene-mcp
MCP server for MyGene.info API |
|
Experimental |
| 34 |
ToxMCP/comptox-mcp
MCP server for the EPA CompTox API (chemical, exposure, hazard, predictive tooling). |
|
Experimental |
| 35 |
ToxMCP/oqt-mcp
MCP server for OECD QSAR Toolbox workflows with structured outputs and PDF reports. |
|
Experimental |
| 36 |
nickzren/mydisease-mcp
MCP server for MyDisease.info API |
|
Experimental |
| 37 |
nickzren/mychem-mcp
MCP server for MyChem.info API |
|
Experimental |
| 38 |
dogeplusplus/bio-agents-mcp
MCP servers for Protein Data Bank, ChemBL, and other life science data... |
|
Experimental |
| 39 |
agentcures/refua-mcp
Model Context Protocol server exposing typed Refua tools for folding,... |
|
Experimental |
| 40 |
pansapiens/uniprot-unipressed-mcp
An MCP server to query Uniprot from your favorite LLM agent |
|
Experimental |
| 41 |
Babajan-B/BioQC-MCP
Professional MCP server for FastQC and MultiQC quality control analysis with... |
|
Experimental |
| 42 |
lukasmki/chemspace-mcp
MCP server enabling AI agents to search for synthesizable building blocks... |
|
Experimental |
| 43 |
AiAgentKarl/bioinformatics-mcp-server
MCP server for bioinformatics data — genes, proteins, PubMed, ClinVar and... |
|
Experimental |
| 44 |
MacromNex/amber_mcp
AMBER MCP server for molecular dynamics simulations and analysis |
|
Experimental |
| 45 |
MacromNex/interpro_mcp
InterProScan MCP server for protein domain and functional analysis |
|
Experimental |