Protein Engineering
XineProtein logo XineProtein

Design Proteins
With Intelligence

XineProtein is a closed-loop AI platform for designing, folding, evaluating, and optimizing novel proteins. From therapeutic antibodies to industrial enzymes — rational protein engineering at computational scale.

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To Optimized Variant
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Design Hit Rate
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Variants Evaluated / Hour
<1Å
Structure Prediction RMSD

Protein Engineering is
Still Trial and Error

Directed evolution campaigns test thousands of random variants to find improvements. It's slow, expensive, and leaves most of the sequence space unexplored.

1-5% Hit Rate in Directed Evolution

Traditional approaches test thousands of variants to find a handful of improvements. Most of the experimental budget is wasted on dead ends.

Structure ≠ Design

AlphaFold predicts what a protein looks like. But designing a new protein with specific function requires a fundamentally different approach.

$500-5,000 Per Variant

Physical characterization of each protein variant is expensive. Computational pre-screening can eliminate 90% of experimental cost.

The XineProtein
Design Loop

Define Function

Specify your target protein function: binding target, catalytic activity, stability requirements. Upload a starting sequence or describe the desired fold.

AI Designs Variants

Our protein language model generates thousands of sequence variants, each predicted to improve your target function while maintaining foldability and expression.

Fold & Simulate

Instant structure prediction validates each variant folds correctly. GPU-accelerated MD simulations assess stability, dynamics, and binding in realistic conditions.

Optimize & Export

Multi-objective optimization refines variants over 100+ autonomous cycles. Top candidates are exported as codon-optimized DNA sequences ready for synthesis.

A Foundation Model for Proteins

Our protein language model understands the relationship between sequence, structure, and function. Trained on billions of protein sequences, it predicts the effect of any mutation without explicit structural modeling.

Zero-shot mutation prediction — predict stability and function effects without training data for your specific protein
Conditional sequence generation — generate novel sequences conditioned on desired function, fold, or binding interface
Functional embedding space — embed and cluster proteins by function, not just sequence similarity
100K+ sequences/hour — evaluate massive variant libraries computationally before any wet lab work
Protein language model

Purpose-Built for Therapeutics

A specialized module for designing therapeutic antibodies. Optimize CDR loops, predict humanization outcomes, and assess developability — all computationally.

CDR loop design — generate and optimize complementarity-determining regions for target binding
Humanization scoring — predict immunogenicity and guide humanization with >90% binding retention
VH/VL pairing — optimize heavy/light chain pairing for stability and expression
Developability assessment — aggregation propensity, viscosity, polyreactivity, thermal stability
Antibody design

From Computation to Synthesis in One Click

Export designed protein variants directly to your synthesis partner. Our platform generates everything needed to go from silico to vitro.

Codon optimization — organism-specific codon optimization for E. coli, CHO, HEK293
Construct design — automated construct design with tags, linkers, and signal peptides
Plate layout generator — 96-well and 384-well plate layouts for expression screening
Assay protocol generation — automated SPR, BLI, DSF protocols for characterization
DNA synthesis export

Ready for Expression and Assay

XineProtein outputs are designed to move directly into synthesis, expression screening, and functional characterization.

DNA-Ready Exports

Codon-optimized constructs and plate layouts reduce handoff friction for synthesis partners.

Assay Planning

Recommended SPR, BLI, DSF, activity, or expression assays match the design objective.

Risk Flags

Aggregation, immunogenicity, expression, and stability risks are surfaced before lab spend.

Protein Programs We Support

Antibodies

Optimize CDRs, humanization, developability, and affinity.

Enzymes

Improve activity, thermostability, solvent tolerance, and substrate scope.

Binders

Design scaffold proteins and biologics against challenging targets.

Industrial Proteins

Balance performance, expression, and manufacturing constraints.

Keep Scientists in the Loop

Protein engineering campaigns work best when AI-generated variants are reviewed alongside domain intuition and assay realities.

Interactive review of sequence clusters and structural hypotheses
Campaign constraints for motifs, liabilities, and expression systems
Feedback loops from assay results into subsequent design rounds
Protein engineering collaboration

XineProtein FAQ

Can I start with a seed sequence?+

Yes. Campaigns can begin from a known sequence, structure, homolog family, or desired functional specification.

Are antibody workflows supported?+

Yes. XineProtein includes antibody-specific CDR design, humanization, developability, and pairing workflows.

How does wet-lab feedback improve designs?+

Assay results can be imported to update objectives and guide the next generation of variants.

Design Your Next Protein

See XineProtein in action. Free pilot campaign for qualified protein engineering teams.