Kairos

The AI-scientist agent on the Evolrix AI biomanufacturing platform. v0.4

June 28, 2026

Kairos is the AI-scientist agent on the Evolrix AI biomanufacturing platform. Give it a protein; it returns a panel of synthesis-ready coding-sequence candidates — each with a transparent scorecard and risk flags, not one opaque "optimized" sequence. Every candidate provably encodes the exact protein, and every score is a deterministic computation you can re-run over the printed sequence.

Scope — Dry-lab design ranking: synthesis safety, host resemblance, 5′ translation initiation, and protein liabilities. Not an expression or titer prediction. Real expression awaits wet-lab data.

How it scores

Four explainable axes — never one fragile score.

Each candidate is scored on four independent axes, every one a deterministic, re-runnable computation with its provenance shown.

01

Manufacturability

GC window, homopolymers, tandem repeats, restriction sites, forbidden motifs.

02

Host-likeness

A genome-derived K. phaffii codon model (codon usage + %MinMax rhythm + codon-pair bias) that deliberately rejects naive max-CAI over-optimization.

03

5′ translation initiation

Start-proximal mRNA accessibility — an open start means better initiation.

04

Protein developability

Length, MW, pI, cysteines, N-glycosylation motifs, hydrophobicity.

EvoCodon

A self-developed, genome-learned codon model.

Candidates are proposed by transparent host heuristics and EvoCodon — a self-developed, genome-learned codon model trained on public K. phaffii genomes that reproduces host-specific codon rhythm beyond frequency-based methods. The learned candidate competes on the same scorecard as every other — it does not auto-win.

Secretion design.

For a secreted protein, Kairos selects a source-traceable secretion leader — e.g. the S. cerevisiae α-mating-factor prepro (UniProt P01149) or the SUC2 invertase signal (UniProt P00724), each carrying its UniProt record and supporting literature — fuses it N-terminally, and designs the coding sequence of the whole construct. Correct by construction: the design encodes exactly signal + target. Kairos chooses a traceable leader and yields a valid construct; it does NOT predict secretion efficiency — that awaits wet-lab data.

Featured run

A Kairos design run on Cytochrome c.

UniProt Q6Q4H8 — a native Komagataella phaffii protein. Twelve reproducible candidates, ranked across all four axes, with the recommended one in the top Pareto tier.

Pichia CDS design report design_50a60d8960 komagataella_phaffii 110 aa · 12 candidates
Dry-lab design ranking — synthesis safety · host resemblance · 5′ initiation · protein liabilities. Not an expression or titer prediction.

Cited evidence retrieved live from the Kairos knowledge layer — every entry a real, openable source.

PMID:41591157

AOX1 promoter regulation

Methanol-induced, glucose-repressed (cis/trans regulation) — grounds the expression strategy.

PMID:37888283

Nitrogen source & MUT pathway

Ammonium sulfate raises MUT / PEX gene expression — tune nitrogen to up-regulate the pathway.

PMID:38650288

Fed-batch strategy

Glycerol for biomass, then methanol induction — the standard Pichia fermentation rhythm.

PMID:31590267

Proteolysis risk

Proteolytic degradation of recombinant protein (HSA) in P. pastoris — watch degradation; add inhibitors if needed.

Recommended

method: uniform top Pareto tier flag: extreme_pi
Candidate panel — top of the Pareto ranking
RankMethodPareto tierFlags
1uniformtop1
2host_weightedtop1
3gc_balancedtop1
4gc_balancedtop2
5host_weightedtop3
Sequence validity strong · clean translates to the exact target protein; in-frame; no premature stop
Manufacturability strong · clean GC window, homopolymers, tandem repeats, restriction sites, forbidden motifs
Host-likeness moderate · clean genome-derived codon usage + %MinMax rhythm + codon-pair bias (rejects max-CAI degenerates)
Protein developability strong · 1 flag length, MW, pI, cysteines, N-glycosylation sequons, hydrophobicity
Every candidate is synonymous — encodes the exact input protein (verified by translation). Ranking is multi-objective (Pareto) with per-criterion explanations: multiple candidates, never one opaque "best". The extreme_pi flag on the winner is an intrinsic property of the target protein, not a design defect. Sequence withheld in the public report; available to invited collaborators. Engine: Kairos v0.1.0.

FAQ

Can it design secreted proteins?

Yes. Kairos selects a source-traceable secretion signal peptide, fuses it, and designs the full construct's CDS. It chooses the leader and guarantees a valid construct; real secretion efficiency is wet-lab, not predicted.

References

Sources behind the design.

The host heuristics, secretion leaders, and host-likeness model draw on public, traceable literature and reference databases. Each is a real, citable source.

  1. UniProt P01149 — S. cerevisiae α-mating-factor prepro. UniProt:P01149
  2. UniProt P00724 — SUC2 invertase signal. UniProt:P00724
  3. Merkaš M, et al. The MFα signal sequence in yeast-based protein secretion: challenges and innovations. Appl Microbiol Biotechnol, 2025. PMID:40471355
  4. Aw R, et al. A systematic analysis of the expression of the anti-HIV VRC01 antibody in Pichia pastoris through signal peptide optimization. Protein Expr Purif, 2018. PMID:29601964
  5. Ahmad M, et al. Efficient Expression of Lactone Hydrolase Cr2zen for Scalable Zearalenone Degradation in Pichia pastoris. Toxins (Basel), 2025. PMID:41591157
  6. Zha J, et al. Advances in Metabolic Engineering of Pichia pastoris Strains as Powerful Cell Factories. J Fungi (Basel), 2023. PMID:37888283
  7. Maity N, et al. Statistically Designed Medium Reveals Interactions between Metabolism and Genetic Information Processing for Production of Stable Human Serum Albumin in Pichia pastoris. Biomolecules, 2019. PMID:31590267

Request research access

Kairos is in research preview, Pichia-scoped. We are onboarding industrial R&D teams who need transparent, re-runnable design ranking — not guesses.

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