Eijex MCP

Eijex MCP is a public Model Context Protocol server that exposes Eijex bioinformatics and CDS-design tools to MCP-compatible clients.

Connect

{
  "mcpServers": {
    "eijex": {
      "type": "http",
      "url": "https://mcp.eijex.com/api/mcp"
    }
  }
}

Available Tools

Tool	Description
factorforge_cds_optimize	Generate an in-silico synonymous CDS candidate and sequence metrics
factorforge_cds_compare	Compare multiple public CDS design profiles side-by-side (CAI, GC%, score)
factorforge_cds_batch	Generate CDS candidates for up to 20 sequences in a single request
factorforge_verify_parameter	Research workflow to verify or update a FactorForge design constant
query_pubmed	Search PubMed for scientific literature
query_pdb	Search RCSB PDB for 3D protein structures
query_ncbi	Search NCBI for protein/nucleotide sequences
query_uniprot	Search UniProt for protein sequences and annotations
query_alphafold	Fetch AlphaFold predicted protein structures
query_kegg	Search KEGG for biological pathways
query_clinicaltrials	Search ClinicalTrials.gov for registered trials
query_opentargets	Search Open Targets for drug targets and disease associations
query_fda	Search FDA adverse events and drug labels via OpenFDA
query_reactome	Search Reactome for biological pathways and reactions
query_chembl	Search ChEMBL for bioactive compounds and drug targets
get_model_recommendations	Get AI model recommendations by task type
get_skill_template	Get a reusable skill template for a new project domain
get_operational_prompt_template	Get reusable operational prompt templates

Safety & Privacy

Eijex MCP provides database lookup and in-silico workflow tools only. It does not provide medical, clinical, diagnostic, treatment, regulatory, or legal advice.

Do not submit patient data, confidential partner data, proprietary sequences, or unpublished constructs to the public MCP endpoint. Use local FactorForge or a private MCP deployment for sensitive work.

FactorForge CDS generates in-silico CDS design candidates. It does not guarantee expression, yield, solubility, or biological activity. Wet-lab validation is required.

Related

• FactorForge CDS — Constraint-based CDS design engine for plant CDS design workflows
• mcp.eijex.com — Web UI