AI-Driven Optimization of Protein Activity and Recombinant Expression
AI-Driven Activity-Expression Trade-Off Optimization
Engineering proteins with superior catalytic activity often comes at the cost of reduced recombinant expression. Likewise, variants that express efficiently may exhibit lower activity, making it difficult to identify candidates suitable for both laboratory development and large-scale manufacturing.
Neoncorte Bio combines artificial intelligence, protein language models, and computational protein engineering to optimize protein activity and expression simultaneously, helping researchers identify balanced variants that perform well in both functional assays and production systems.
Our AI-assisted workflows accelerate Design-Build-Test-Learn (DBTL) cycles by prioritizing variants predicted to improve overall performance while reducing unnecessary laboratory screening.
Why Activity and Expression Must Be Optimized Together
Protein engineering programs frequently encounter competing objectives:
- Increased catalytic activity may reduce recombinant expression.
- Higher expression can sometimes compromise catalytic efficiency.
- Stabilizing mutations may improve production while decreasing function.
- Activity-enhancing mutations may introduce folding or solubility challenges.
AI Technologies Behind Our Platform
Neoncorte Bio integrates advanced computational technologies including:
- Protein language models (PLMs)
- Artificial intelligence
- Machine learning
- Structure-informed protein modeling
- Computational mutagenesis
- Virtual Deep Mutational Scanning (DMS)
- Protein fitness landscape prediction
- Epistasis prediction
- Higher-order mutation prediction
- Active learning
- Bayesian optimization
- Pareto optimization
- Multi-objective optimization
Protein Properties Optimized Simultaneously
Our AI platform supports balancing activity with expression while considering additional molecular properties.
Catalytic Activity
Predict mutations that improve enzymatic performance while maintaining overall protein quality.
Expression Yield
Identify variants with improved recombinant production in microbial or mammalian expression systems.
Protein Stability
Improve structural robustness that supports both activity and efficient expression.
Protein Solubility
Reduce insoluble expression and improve downstream purification.
Aggregation Resistance
Lower aggregation propensity during production and storage.
Manufacturability
Support scalable recombinant protein production
Developability
Balance biochemical performance with downstream development requirements.
Thermostability
Improve operational stability without compromising expression.
Predict mutations that improve enzymatic performance while maintaining overall protein quality.
Expression Yield
Identify variants with improved recombinant production in microbial or mammalian expression systems.
Protein Stability
Improve structural robustness that supports both activity and efficient expression.
Protein Solubility
Reduce insoluble expression and improve downstream purification.
Aggregation Resistance
Lower aggregation propensity during production and storage.
Manufacturability
Support scalable recombinant protein production
Developability
Balance biochemical performance with downstream development requirements.
Thermostability
Improve operational stability without compromising expression.
AI-Assisted Optimization Workflow
Our computational workflow combines complementary AI technologies.
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Computational MutagenesisPredict the functional effects of mutations before laboratory experiments. -
Virtual Deep Mutational ScanningEvaluate millions of sequence variants computationally. -
Protein Fitness Landscape PredictionIdentify mutation pathways that preserve both activity and expression. -
Epistasis PredictionModel interactions between multiple mutations that influence protein behavior. -
Higher-Order Mutation PredictionEvaluate combinations of mutations that outperform individual substitutions. -
Active LearningContinuously improve predictive accuracy using newly generated experimental data.
Applications
Our activity-expression optimization workflows support:
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Industrial Enzyme Engineering
Improve enzyme productivity while maintaining manufacturing efficiency. -
Therapeutic Protein Engineering
Balance biological function with recombinant production. -
Synthetic Biology
Improve protein production in engineered microorganisms. -
Antibody Engineering
Optimize expression while preserving affinity and developability. -
Biocatalyst Development
Engineer enzymes suitable for large-scale industrial applications.
Design-Build-Test-Learn (DBTL) Collaboration
Our computational platform integrates prediction with experimental validation.
Design
Analyze sequences, structures, and engineering objectives.
Build
Prioritize mutations and focused variant libraries.
Test
Experimentally evaluate engineered proteins.
Learn
Retrain predictive models using new laboratory data.
Each DBTL cycle improves prediction quality while reducing unnecessary experimental screening.
Analyze sequences, structures, and engineering objectives.
Build
Prioritize mutations and focused variant libraries.
Test
Experimentally evaluate engineered proteins.
Learn
Retrain predictive models using new laboratory data.
Each DBTL cycle improves prediction quality while reducing unnecessary experimental screening.
Why Choose Neoncorte Bio?
Neoncorte Bio combines expertise in:
- Artificial intelligence
- Machine learning
- Protein language models
- Computational protein engineering
- Structural biology
- Computational mutagenesis
- Virtual Deep Mutational Scanning
- Protein fitness landscape prediction
- Epistasis prediction
- Higher-order mutation prediction
- Active learning
- Bayesian optimization
- Pareto optimization
- Multi-objective optimization
- Design-Build-Test-Learn (DBTL)
Who We Work With
Our platform supports:
- Biotechnology companies
- Pharmaceutical companies
- Industrial enzyme manufacturers
- Synthetic biology companies
- Antibody developers
- CROs and CDMOs
- Industrial biotechnology organizations
- Academic research institutions
Frequently Asked Questions (FAQs)
Our platform harnesses advanced artificial intelligence and machine learning to design, optimize, and engineer proteins tailored to your specific requirements. Whether you need improved enzyme efficiency, novel protein functions, or tailored biotherapeutics, our solutions streamline the protein design process and reduce time-to-market.
Our services are ideal for biotechnology and pharmaceutical companies, academic research labs, industrial manufacturers, and any organization involved in protein-based product development. Applications include enzyme optimization, biocatalyst development, therapeutic protein design, and more.
The process begins with your input data, such as protein sequences, structural information, and desired functional attributes. Our AI algorithms then generate a library of potential protein variants and use predictive modeling to evaluate their stability, activity, and specificity. The top candidates are ranked and provided for further experimental validation, thereby reducing the number of required lab iterations.
Our platform is versatile and can be applied to a wide range of proteins, including enzymes, structural proteins, and therapeutic proteins. We can optimize existing proteins or design novel ones for applications in catalysis, biopharmaceuticals, diagnostics, and more.
Absolutely. We work closely with you to tailor our AI models and algorithms to your target proteins and desired outcomes. This includes integrating proprietary data and fine-tuning parameters to ensure that our platform delivers the most relevant and high-performing protein candidates for your application.
Our platform offers robust API support and standard data export formats (e.g., CSV, JSON) to seamlessly integrate with your Laboratory Information Management Systems (LIMS) and other data analytics pipelines. We also provide comprehensive onboarding and training to ensure a smooth adoption process.
Our models are trained on extensive datasets of protein interactions, structural data, and experimental results. We continuously refine our algorithms with real-world feedback to improve prediction accuracy. While our computational predictions are highly reliable, we recommend subsequent in vitro or in vivo validation to confirm the performance of the engineered proteins.
Yes, we provide collaborative support throughout the validation process. Our team can help design proof-of-concept studies and coordinate with your wet lab partners to verify the performance of our predicted protein variants.
We offer flexible pricing models based on the scope and duration of your project. Options include subscription-based plans for ongoing R&D, as well as project-specific pricing for one-off protein engineering campaigns. Please contact us for a personalized consultation and detailed quote.
Our dedicated customer support team is available to assist you at every stage—from initial onboarding and technical training to troubleshooting and ongoing optimization. We offer support via email, phone, and live chat, along with detailed documentation and a comprehensive FAQ section.
Balance Protein Performance and Production with AI
Contact Neoncorte Bio to discuss your activity-expression optimization project
Neoncorte Bio
Where AI Meets Biotechnology
Neoncorte Bio is at the forefront of the convergence between artificial intelligence and enzyme engineering. Our team comprises experts in computational biology, bioinformatics, and machine learning, all driven by a mission to accelerate innovation in enzyme design. By leveraging our advanced AI models, we provide unparalleled solutions that enhance efficiency, reduce costs, and push the boundaries of what's possible in enzyme engineering
Proud Member of Leading Global AI Programs
Neoncorte Bio is part of the NVIDIA Inception and Nebius for Startups programs — two of the world’s leading ecosystems for high-performance AI innovation. These partnerships strengthen our ability to deliver next-generation AI-driven protein, enzyme, and aptamer engineering.
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As a member of NVIDIA Inception, Neoncorte Bio gains access to cutting-edge GPU technologies, expert guidance, and a global AI ecosystem that supports companies from prototype to production. The program empowers us to explore new AI opportunities and build high-performance biological design pipelines powered by NVIDIA’s world-class platform. -
Through Nebius for Startups, we gain access to high-performance compute infrastructure optimized for large-scale AI workloads, along with hands-on technical guidance and a strong community of innovative AI companies. Nebius enables us to train and deploy complex biological models more efficiently — accelerating enzyme, protein, and aptamer design while supporting rapid scaling of our R&D pipelines.
Publications
Scientific Publication of Neoncorte Bio Team
- Modification of natural enzymes to introduce new properties and enhance existing ones is a central challenge in bioengineering. This study is focused on the development of Taq polymerase mutants that show enhanced reverse transcriptase (RTase) activity while retaining other desirable properties such as fidelity, 5′-3′ exonuclease activity, effective deoxyuracil incorporation, and tolerance to locked nucleic acid (LNA)-containing substrates.
- The transcriptomic data are being frequently used in the research of biomarker genes of different diseases and biological states. The most common tasks there are the data harmonization and treatment outcome prediction. Both of them can be addressed via the style transfer approach. Either technical factors or any biological details about the samples which we would like to control (gender, biological state, treatment, etc.) can be used as style components.
- List of all Neoncorte Bio publications dedicated to Molecular Biology, Biotechnology, Artificial Intelligence and Artificial Neural Networks, published mostly by Nikolay Russkikh, CEO of Neoncorte Bio
Our Expertise in Action
With extensive experience in AI applications and software engineering tailored to the life sciences, we specialize in solving complex challenges and delivering innovative solutions for our customers. Our work demonstrates a deep understanding of cutting-edge technologies and their application in the real world.
Here are examples of the types of projects we have successfully delivered:
Here are examples of the types of projects we have successfully delivered:
- Automated NGS Data Analysis:Designed a production-grade solution for the automated processing, annotation, and analysis of Next-Generation Sequencing (NGS) data.
- Single-Cell Data Integration:Built state-of-the-art tools for integrating multimodal single-cell data, achieving recognition for technical excellence.
- Metagenomic Classification Algorithms:Developed advanced methods for classifying sequencing reads in metagenomics research.
- High-Throughput Image Processing Pipelines:Engineered an efficient pipeline to process millions of sequencing images with exceptional accuracy.
- Cell Counting via AI:Created a computer vision solution for precise cell counting in microphotography images, streamlining data analysis.
Get in touch with our team
Phone: +1-503-754-3958
Email: contact@neoncorte.com
Email: contact@neoncorte.com
© All Rights Reserved. Neoncorte Bio. 2024-2026
contact@neoncorte.com
contact@neoncorte.com