1DP · Sequence-based design
Public MCP toolsProtein sequence + design constraints → CDS candidates and computational checks.
Use the CDS design tools below. Their existing engine and profile settings remain unchanged.
View sequence design tool →BioDesign Execution Layer
Eijex MCP
Turns scientific context into reviewable CDS candidates, pre-synthesis checks, and lookup results
For research and in-silico use only. FactorForge tools support reviewability and reproducibility; outputs are design-review artifacts, not experimental validation, synthesis-acceptance decisions, regulatory advice, or comparative biological-performance evidence. Do not submit patient data, confidential partner data, proprietary sequences, or unpublished constructs to this public endpoint.
One platform, two design modes
1DP and 3DP are optimization workflows, not separate agents or MCP servers. The tester chooses the mode; the workflow does not automatically choose a winning candidate.
3DP · Structure-conditioned design
Experimental · browser test pathProtein + uploaded structure + reviewed positions → 1DP comparator and structure-conditioned candidate.
Direct FactorForge browser testing uses an uploaded exact-match PDB/mmCIF chain and reviewed protein positions, without ResearchOS approval or ValidationHub recording. This MCP endpoint does not currently execute 3DP. FactorForge uses its built-in default policy; custom SOP management is paused.
The browser can suggest positions from declared structure confidence observations; users must accept and review them. Both modes report RNA motif scans and initiation-window MFE when available. These observations do not establish expression or folding benefits.
FactorForge browser UI →Direct testing does not require local ResearchOS. The retained approved research workflow remains available for later operational use.
Retained research workflow (for later operational use)
- 1. ResearchOS
Register inputs, choose a mode and track the request. This is separate from direct browser testing. - 2. AgentOS → FactorForge
Check approval and run the selected optimization workflow. - 3. ValidationHub
Record computational evidence for human review.
PDB and AlphaFold tools retrieve structure information; a lookup does not run 3DP or predict a new structure. Engine generation “Gen 3” does not mean 3DP.
Watermark: disabled in the current testing UI. Custom SOP management is paused; the built-in default policy remains active.
Connection — MCP client settingsJSON
{
"mcpServers": {
"eijex": {
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"url": "https://mcp.eijex.com/api/mcp"
}
}
}CDS design tools
4Callable MCP tools for sequence-based design. Tools are not separate autonomous agents.
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factorforge_cds_optimize
Generate an in-silico synonymous CDS candidate for N. benthamiana.
FactorForgeBiotechDNA
🧭
factorforge_cds_slate
Generate a bounded Top-K computational discovery slate.
FactorForgeDiscoveryResearch Preview
📊
factorforge_cds_compare
Compare multiple FactorForge CDS design profiles side-by-side.
FactorForgeBiotechDNA
⚡
factorforge_cds_batch
Generate CDS candidates for up to 20 protein sequences in a single request.
FactorForgeBiotechDNA
Database lookup tools
7Query biomedical databases — literature, structures, pathways, and trials.
📄
query_pubmed
Search PubMed for scientific literature.
LiteratureResearchBiotech
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query_pdb
Search the RCSB Protein Data Bank for 3D protein structures.
StructureProteinBiotech
🗺️
query_kegg
Search KEGG for biological pathways.
PathwaySystems BiologyBiotech
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query_ncbi
Search NCBI protein or nucleotide database for sequence summaries and accession numbers.
SequenceNCBIBiotech
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query_uniprot
Search UniProt for protein entries — accession, gene names, organism, function, and sequence length.
ProteinUniProtBiotech
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query_alphafold
Fetch AlphaFold structure prediction for a protein by UniProt accession.
StructureAlphaFoldBiotech
IP
query_interpro
Search InterPro for protein domain architecture by UniProt accession.
DomainProteinBiotech
Research workflows
1Multi-step research protocols — structured pipelines with decision gates.
https://mcp.eijex.com/api/mcp