eCOMPASS

De-risk your RNA program from design to clinic.

Q: What if we already use computational design tools?

Standard tools typically optimize to one metric, such as stability or translation. eNAVIGATE is fundamentally different. Our RNA-centric approach enables multiobjective optimization, allowing us to explore the full design space to create therapies tailored to your Target Product Profile.

Q: How is eCOMPASS different from working with a CDMO or an AI design platform?

CDMOs focus on manufacturing. AI design platforms focus on sequence optimization. eCOMPASS connects design, prototyping, and characterization so that validation data feeds directly into the next design cycle. You get a single partner from amino acid sequence to characterized candidate, not a chain of handoffs.

Q: What's the ROI on switching from our current approach?

A candidate that fails in late-stage manufacturing due to undetected impurities or poor protein expression can cost millions and set a program back months to years. eCOMPASS catches those issues early, before they can halt programs. Partners who engage at program start routinely find the investment is small relative to a single avoided failure.

Q: How do you handle IP and sequence confidentiality?

Your proprietary sequences and program details are never shared. We work with major pharma legal teams regularly and can accommodate your standard CDA/NDA requirements.

Design, prototype, and characterize in an integrated loop. Every cycle generates empirical data that makes the next candidate better.

Get Started

Lead Candidate

Design

Make

Characterize

Tailored to your TPP

Multidimensional sequence design optimizes yield, translation efficiency, and stability together, not one metric at a time.

Fewer late-stage surprises

Liabilities and bottlenecks identified before manufacturing scale-up, while you can still act on them.

Evidence-backed candidates

Every candidate arrives with empirical data on potency, purity, and stability. You move forward with confidence, not assumptions.

The Platform

From target to candidate.

Many RNA programs rely on standard approaches to sequence design and only discover dsRNA impurities, structural liabilities, or translation bottlenecks after manufacturing, when the cost to fix them is highest. eCOMPASS replaces that fragmented approach with a single partner that integrates AI-driven design, in-house prototyping, and sequencing-based characterization in a closed loop. You provide the amino acid sequence, and each cycle of empirical data produces a better candidate than the last.

Design

AI-driven RNA sequence optimization, balancing yield, expression, stability, and specificity to generate candidates tuned to your Target Product Profile.

Make

In-house manufacturing gets you from design to testable material fast. When you're ready to scale, we connect you to validated manufacturing partners.

Characterize

Nucleotide-level characterization from proprietary assays available nowhere else. Know not just what went wrong but why, from dsRNA sources to ribosome stalls.

Every lab-in-the-loop cycle provides a better candidate.

Design predicts. Validation confirms.

Even the most sophisticated sequence optimization produces candidates that should work, but dsRNA hotspots, ribosome stalls, and structural liabilities only emerge after synthesis. eCOMPASS closes that gap, feeding what characterization finds back into the next design cycle so each iteration is better by measurement, not just by prediction. That's the difference between a prediction and a decision you can defend.

Data You Can Act On

Every cycle generates mechanistic insight, not just scores.

eCOMPASS generates over 150,000 data points per target amino acid sequence, covering identity, purity, potency, stability, and safety. These are some of the insights that drive candidate optimization and selection.

Screen

Identify limitations before manufacturing

In silico analytics predict hydrolysis hotspots so unstable candidates are deprioritized before manufacturing. After in vitro transcription, those predictions are validated with sequencing analytics that directly measure breakage sites.

Purity

Identify the source of dsRNA impurities

Sequencing analytics pinpoint the exact nucleotide positions where dsRNA originates, enabling targeted changes to reduce immunogenicity risk.

Stability

Understand what drives drug stability

Chemical probing measures RNA secondary structure at single-base resolution, identifying regions that affect drug stability.

Translation

Map ribosome activity across the RNA

Ribosome profiling maps ribosome dynamics across the full sequence, identifying pause sites and codon-level bottlenecks that limit protein output.

Platform Results

eCOMPASS in action.

This case study demonstrates eCOMPASS with the development of a gene editing therapy. We have also supported vaccine, CAR-T, and protein replacement programs for major biopharmas and biotechs.

eCOMPASS Case Study

Multidimensional design outperforms single-metric optimization.

Cas9 mRNA sequences were optimized to balance yield, expression, and stability. Candidates were prototyped and characterized in-house. The resulting candidates outperformed both the baseline design and competing designs.

400%

Protein expression increase vs. competing designs

58%

Cas9 editing efficiency increase over baseline

End-to-End

Our process.

You bring the program. We align on what success looks like, then iterate through design, prototyping, and characterization until your candidate is ready to advance. Most programs reach a characterized candidate within two to three cycles.

eCOMPASS process workflow: Your program leads to defining success criteria together, then enters an iterative Design, Make, Characterize loop that produces a characterized lead candidate ready to advance to pre-clinical

Inside the platform

A closer look at each stage of eCOMPASS.

01 Design: eNAVIGATE +

01 — Design

eNAVIGATE: AI That Understands RNA Biology

Optimizes across IVT yield, expression, stability, and cell-type specificity simultaneously, using models trained on proprietary experimental data. The result: multiple candidates tuned to your Target Product Profile, then characterized with eMERGE's sequencing-based analytics.

Explore eNAVIGATE

eNAVIGATE multidimensional optimization — Four optimized designs for the same protein, each tuned to a different performance priority

02 Make: Rapid Prototyping +

02 — Make

Rapid Prototyping: Design to Testable Material

In-house RNA manufacturing, including linear mRNAs over 10 kb, gets you from optimized design to testable material quickly. QC confirmation of yield and integrity at every step.

Once you've selected a lead candidate, we provide a pathway to scale through our validated manufacturing partners.

Explore RNA manufacturing

Fragment analyzer trace showing high yield and integrity from a synthesized RNA, suitable for validation and iterative design

03 Characterize: eMERGE +

03 — Characterize

eMERGE: Beyond Standard QC

Standard QC assays tell you a molecule passed. eMERGE tells you why it passed or failed, and how it can be improved. Proprietary sequencing-based assays provide nucleotide-level resolution across major CQAs including dsRNA impurities and RNA secondary structure.

The result: actionable data that explains candidate behavior, not just a pass/fail readout. Every finding then feeds directly into the next design cycle.

Explore eMERGE

RNA secondary structure comparison across LNP formulations — RNA secondary structure measured across different LNP formulations, revealing how delivery vehicle composition affects RNA stability

Our Track Record

Trusted and proven.

2017

Supporting RNA drug development for almost a decade

300+

Partners have trusted Eclipsebio across pharma, biotech, and academia

80%

Of top biopharma companies have worked with Eclipsebio

FAQ

Common questions about eCOMPASS.

What if we already use computational design tools?

What if we already have in-house characterization?

eMERGE complements standard QC with proprietary sequencing-based assays: chemical probing for RNA secondary structure, ribosome profiling for translation dynamics, and dsRNA mapping to pinpoint immunogenicity sources at single-nucleotide resolution. These address critical quality attributes across identity, purity, potency, stability, and safety that traditional HPLC, CGE, or ELISA-based methods cannot resolve. Most partners use eMERGE as a complement to their existing analytics.

How is eCOMPASS different from working with a CDMO or an AI design platform?

What's the ROI on switching from our current approach?

How many cycles does a typical project take?

How do you handle IP and sequence confidentiality?

Ready to de-risk your RNA program?

We'll connect you with an RNA expert to explore how eCOMPASS fits your development goals.

Please email info@eclipsebio.com to discuss your program.