Eijex MCP is a public Model Context Protocol server that exposes Eijex bioinformatics, literature lookup, and FactorForge CDS design/review tools to MCP-compatible clients.
The gateway keeps product and engine versions separate. FactorForge optimization uses its public HTTP API; product/engine provenance comes from the response. No Python executable, local model path or shared database is required on Vercel. Research modes remain subject to the upstream feature gate and return MCP tool errors when unavailable. Public MCP requests do not persist designs.
Development checks: npm test, npm run lint, npm run build (Node.js 24).
MCP 1.4.2 was deployed on 2026-10-08. Public endpoint checks confirmed profile
and explicit DP v2.1.1 optimization, upstream provenance and save_db rejection.
These synthetic engineering checks do not establish experimental performance.
{
"mcpServers": {
"eijex": {
"type": "http",
"url": "https://mcp.eijex.com/api/mcp"
}
}
}| Tool | Description |
|---|---|
factorforge_cds_optimize |
Generate an in-silico synonymous CDS candidate with Rule, DP v2, or explicit DP v2.1.1 local-guard engine selection and pre-synthesis review metrics |
factorforge_cds_slate |
Generate a research-only Top-K candidate slate with explicit generator and evidence boundaries |
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 |
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 and pre-synthesis review artifacts. Outputs are design-review artifacts, not experimental validation, synthesis-acceptance decisions, regulatory advice, or comparative biological-performance evidence.
- FactorForge CDS — CDS design and pre-synthesis sequence review with the v3.3.0 NbeV1.1 high-confidence CDS-derived active default
- mcp.eijex.com — Web UI
- Sponsor — Support our research via GitHub Sponsors or PayPal
- GitHub Issues — bugs, features: github.com/eijex/eijex-mcp/issues
- Email — eijex.lab@gmail.com
- FactorForge — factorforge.eijex.com
- Lab — www.eijex.com
The homepage distinguishes public CDS/lookup tools from the local approved 1DP/3DP workflow. PDB/AlphaFold lookup does not imply execution of experimental 3DP. Watermark is paused in current testing. Removed homepage catalog entries for evaluate_sequence and optimize_protein_slm: these names are not registered tools in this server's actual MCP handler. Existing registered tools and profile/engine enums are unchanged. Local 3DP is not newly exposed through the public endpoint.
Homepage UI distinguishes callable CDS design tools from local 1DP/3DP workflows. These modes do not require separate autonomous agents or MCP servers. 3DP execution is not exposed by the public MCP endpoint; the local operator must prepare ResearchOS and registered inputs. These homepage edits are unreleased.
Job 389 supersedes the Job 388 local-only browser routing: the FactorForge source now implements direct stateless 3DP browser/API testing with uploaded exact-match structure and reviewed positions. No ResearchOS approval or ValidationHub record is collected in this test path. It is unreleased; public MCP tools do not yet expose this execution mode.