生物信息学模型协议服务器

https://heuris-biomcp.onrender.com/mcp

https://heuris-biomcp.onrender.com/mcp

{
  "mcpServers": {
    "heuris-biomcp": {
      "url": "https://heuris-biomcp.onrender.com/mcp"
    }
  }
}

You -> "What drugs target EGFR and what clinical trials are recruiting?"
ChatGPT + Heuris-BioMCP -> Queries ChEMBL + ClinicalTrials.gov -> Structured answer

https://heuris-biomcp.onrender.com/mcp

https://heuris-biomcp.onrender.com/sse

# Clone the repository
git clone https://github.com/SachinGawande2003/Heuris-BioMCP.git
cd Heuris-BioMCP

# Install (standard)
pip install -e .

# Install with neuroimaging support
pip install -e ".[neuroimaging]"

# Install with dev dependencies (recommended)
pip install -e ".[dev]"

{
  "mcpServers": {
    "heuris-biomcp": {
      "command": "biomcp",
      "env": {
        "NCBI_API_KEY": "your_ncbi_api_key_here"
      }
    }
  }
}

https://heuris-biomcp.onrender.com/mcp

https://heuris-biomcp.onrender.com/sse

"Search PubMed for recent papers on CAR-T cell therapy in B-cell lymphoma"
"Get the AlphaFold structure for TP53 and tell me about the confidence scores"
"What drugs are approved that target EGFR?"
"Generate a multi-omics report for KRAS"
"Predict the structure of EGFR with ligand CC1=CC=CC=C1 and compute binding affinity"
"Generate a DNA sequence starting with ATGGCG..."

"Search PubMed for BRCA1 CRISPR correction methods published in the last 2 years"
"Find review articles about PD-1/PD-L1 immune checkpoint inhibitors"

"Get UniProt info for human TP53 (P04637) including its domains and disease associations"
"Search for AlphaFold structures for insulin receptor"
"Find all PDB crystal structures of BRAF kinase domain resolved below 2.5 Ångström"

"What are the top ChEMBL compounds targeting KRAS G12C mutation?"
"Get compound info for imatinib (CHEMBL941)"
"Show me gene-disease associations for BRCA1 with evidence scores"

"Predict the 3D structure of insulin (sequence: ...) with ligand CCO"
"Compute binding affinity between EGFR and gefitinib (SMILES: ...)"
"Get structure prediction for a protein-protein complex"

"Generate a 200bp promoter sequence starting with ATG"
"Compare wildtype vs variant DNA sequence for TP53 mutation"
"Generate regulatory element for gene expression"

"Generate a complete multi-omics report for EGFR"

"Get OMIM diseases associated with TP53"
"Show STRING protein interactions for EGFR"
"Get GTEx expression data for BRCA1 across tissues"
"Find mutations in TP53 from cBioPortal"
"Search GWAS for diabetes-associated SNPs"

"Verify the claim that TP53 is a tumor suppressor gene"
"Detect conflicts between OMIM and DisGeNET for BRCA1"

"Generate an experimental protocol for CRISPR knockout of BRCA1"
"What cell lines should I use to study KRAS mutations?"
"Calculate sample size for detecting 2-fold change with p<0.05"

"What's the knowledge graph from our conversation so far?"
"Find biological connections between TP53 and EGFR"
"Export our research session as a reproducible script"
"Plan and execute a research workflow for PD-1 drug targets"

biomcp/
├── src/biomcp/
│   ├── server.py              # MCP server — tool registry & dispatcher
│   ├── tools/
│   │   ├── ncbi.py            # PubMed, Gene, BLAST
│   │   ├── proteins.py        # UniProt, AlphaFold, PDB
│   │   ├── pathways.py        # KEGG, Reactome, ChEMBL, Open Targets
│   │   ├── advanced.py        # ClinicalTrials, GEO, scRNA, Ensembl,
│   │   │                      # Multi-Omics, Neuroimaging, Hypothesis
│   │   ├── nvidia_nim.py      # Boltz-2, Evo2-40B AI models
│   │   ├── databases.py       # v2: OMIM, STRING, GTEx, cBioPortal,
│   │   │                      #      GWAS, DisGeNET, PharmGKB
│   │   ├── verify.py          # v2: Claim verification, conflict detection
│   │   └── protocol_generator.py  # v2: Experimental design tools
│   ├── core/
│   │   ├── entity_resolver.py # v2: Cross-database entity resolution
│   │   ├── knowledge_graph.py # v2: Session knowledge graph
│   │   └── query_planner.py   # v2: Adaptive query planner
│   └── utils/
│       └── __init__.py        # Rate limiter, cache, validators, HTTP client
├── tests/
├── pyproject.toml
└── README.md

# Development setup
pip install -e ".[dev]"

# Run tests
pytest tests/ -v --cov=biomcp

# Lint + type check
ruff check src/
mypy src/

@software{biomcp2025,
  title   = {Heuris-BioMCP v2: A Comprehensive MCP Server for Bioinformatics, AI Models, and Life Sciences},
  year    = {2025},
  url     = {https://github.com/SachinGawande2003/Heuris-BioMCP},
  license = {MIT}
}