BioDesign Execution Layer

Eijex MCP

Turns scientific context into validated CDS and construct design artifacts

Connection — .mcp.json / Claude Code settingsJSON

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

Agents

Execute design tasks — call external engines and return validated artifacts.

🧬

factorforge_optimize_cds

Optimize a protein sequence into a codon-adapted DNA CDS for N. benthamiana.

FactorForgeBiotechDNA

Skills

Query biomedical databases — literature, structures, pathways, and trials.

📄

query_pubmed

Search PubMed for scientific literature.

LiteratureResearchBiotech

🔬

query_pdb

Search the RCSB Protein Data Bank for 3D protein structures.

StructureProteinBiotech

🗺️

query_kegg

Search KEGG for biological pathways.

PathwaySystems BiologyBiotech

🏥

query_clinicaltrials

Search ClinicalTrials.gov for registered clinical trials.

ClinicalTrialsResearch

🧫

query_ncbi

Search NCBI protein or nucleotide database for sequence summaries and accession numbers.

SequenceNCBIBiotech

🔗

query_uniprot

Search UniProt for protein entries — accession, gene names, organism, function, and sequence length.

ProteinUniProtBiotech

🧩

query_alphafold

Fetch AlphaFold structure prediction for a protein by UniProt accession.

StructureAlphaFoldBiotech

🎯

query_opentargets

Search Open Targets Platform for gene targets or diseases and their associations.

TargetDiseaseBiotech

💊

query_fda

Search OpenFDA for drug adverse events and labels.

FDADrug SafetyCandidaX

🔬

query_reactome

Search Reactome for curated biological pathways.

PathwaysSystems BiologyFactorForge

💊

query_chembl

Search ChEMBL for bioactive compounds and drug targets.

ChEMBLDrug DiscoveryCompoundBioactivityCandidaX

Workflows

Multi-step research protocols — structured pipelines with decision gates.

🔍

factorforge_verify_parameter

Initialize a structured 0→7 step research workflow to verify or update a FactorForge design constant.

FactorForgeWorkflowVerification

https://mcp.eijex.com/api/mcp