Cradle - AI-powered protein engineering platform for scientists

What is Cradle

If you've ever worked in protein engineering, you know the frustration. Traditional approaches to developing new proteins—whether for therapeutics, industrial enzymes, or vaccines—rely heavily on trial and error. You'd design dozens or hundreds of variants, run wet lab experiments, analyze results, and then start the cycle again. This process can take months or even years, consuming significant resources with no guarantee of success.

That's exactly the challenge Cradle was built to solve.

Cradle is an AI-powered protein engineering platform that helps scientists accelerate their R&D from concept to candidate. Instead of relying solely on exhaustive screening, you can leverage machine learning models trained on both public datasets and your own experimental data to predict which protein designs are most likely to succeed. The result? 2 to 12 times faster development timelines, with candidates that scientists consistently rate 8 out of 10 for performance.

What sets Cradle apart is its ability to simultaneously optimize multiple protein properties—activity, stability, expression level, binding affinity, and more—in a single design round. Rather than trading off one attribute for another, the platform finds solutions that balance all your targets. And because the models learn from your specific experimental data, they get smarter the more you use them.

Over 50 projects have validated these acceleration results, and Cradle is now trusted by leading organizations including Novo Nordisk, Novonesis, Bayer, argenx, AbbVie, Johnson & Johnson, Immunai, and Pfizer. Whether you're a biopharma company developing next-generation antibodies or an industrial biotech firm engineering robust enzymes, Cradle gives your team a powerful edge in bringing better proteins to market faster.

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Core Features That Accelerate Your Protein Engineering

What makes Cradle genuinely useful isn't just the AI technology—it's how that technology translates into real workflow improvements for scientists and R&D teams. Here's what you can actually do with the platform.

Multi-Property Optimization

You can use this feature to simultaneously improve multiple protein attributes in a single design cycle. Instead of optimizing for binding affinity and then separately addressing stability, Cradle's optimization engine balances all your target properties together. This is particularly valuable for antibody affinity maturation, where you need to improve binding strength while maintaining developability and avoiding immunogenicity. For enzyme engineering, it means you can push catalytic activity higher without sacrificing thermal stability or expression yields.

Automated Model Finetuning

Every time you upload experimental results from your lab, Cradle automatically fine-tunes its models to better understand your specific protein of interest. You don't need machine learning expertise—the platform handles the technical work. Starting from a single sequence or a small dataset is perfectly fine; the system uses public pre-training data as a foundation and then adapts to your molecular context. As your experimental database grows, the models become increasingly精准 (precise) at predicting what will work in your specific system.

Intelligent Plate Design

Rather than randomly testing hundreds of variants, you can rely on Cradle's intelligent selection process. The platform runs thousands of virtual simulations to identify the most promising candidates from millions of possible designs, then constructs an optimized experimental plate that maximizes your chance of success. This approach has earned consistently high marks from scientists—those 8 out of 10 ratings we mentioned? They reflect real-world performance in the lab, not just computational predictions.

Advanced Sequence Design Controls

When you need precise control over where mutations occur, Cradle delivers. You can define template sequences, block specific mutations, constrain changes to particular protein regions, and set custom optimization objectives. This level of control matters when you're working with known structural domains that shouldn't be modified, or when you need to avoid certain sequence motifs entirely. The platform supports enzymes, antibodies, and peptides across virtually any protein modality.

Data and Workflow Management

Your laboratory data is valuable, and Cradle helps you manage it properly. The platform offers flexible data management with custom schemas that match your lab's existing workflows, complete audit trails for compliance, and full API access for integration with your other tools. Whether you're working across multiple teams or preparing for regulatory audits, the infrastructure supports your operational needs.

Enterprise-Grade Security

For organizations concerned about IP protection, Cradle provides comprehensive security controls including SSO integration with Google and Microsoft, multi-factor authentication, role-based access permissions, and the robust protections you'd expect from enterprise software. More importantly, your data stays yours—we'll cover this in detail in the security section, but the core principle is straightforward: your intellectual property remains yours with no royalty obligations.

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Who Is Using Cradle

Cradle serves a diverse range of organizations across biopharma, industrial biotechnology, food technology, and academic research. Understanding how others use the platform can help you identify whether it's the right fit for your team.

Biopharma and Antibody Drug Discovery

If you're working in antibody discovery, you likely face the challenge of balancing binding potency with developability. Traditional approaches rely on large screening campaigns that are time-consuming and expensive. With Cradle, you can start from a single sequence or an existing antibody dataset and use AI to generate optimized candidates through affinity maturation. The platform simultaneously considers developability risks—immunogenicity, aggregation potential, post-translational modification sites—so your candidates aren't just potent they're also ready for downstream development.

Enzyme Engineering for Industrial Applications

Industrial enzymes need to perform under challenging conditions: high temperatures, extreme pH levels, or the presence of solvents. You can't afford to sacrifice activity for stability or vice versa. Cradle's multi-property optimization is particularly valuable here, allowing you to find the sweet spot between catalytic performance and environmental robustness. Companies like Novonesis use this capability to develop enzymes for applications ranging from biofuel production to food ingredient manufacturing.

Vaccine Antigen Design

Designing vaccine antigens involves its own unique balance—you need proteins that are stable enough to manufacture and store, yet immunogenic enough to trigger protective immune responses. Cradle helps teams optimize both stability and immunogenicity simultaneously, accelerating the path from antigen identification to candidate selection.

Multi-Specific Antibody Development

Developing bispecific or multi-specific antibodies adds another layer of complexity: you need to optimize binding for multiple targets at once while maintaining proper molecular architecture. Cradle supports virtually all antibody formats—VHH, scFv, Fab, IgG, and bispecific configurations—giving you the flexibility to explore multiple modalities.

Protein Developability Optimization

One of the most frustrating outcomes in protein engineering is investing months developing a candidate only to discover developability issues late in the process. Cradle helps you avoid these costly failures by screening for developability risks early: immunogenicity, aggregation propensity, glycosylation sites, and other liabilities that often surface during late-stage CMC (chemistry, manufacturing, and controls) work.

Academic and Research Applications

Even if your team is just starting out with limited data, Cradle provides value. You can initiate projects from a single sequence, leveraging the platform's pre-trained public models while building your own proprietary dataset. This makes it accessible for academic research groups exploring novel protein engineering challenges without extensive historical data.

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Technical Architecture and Capabilities

Understanding what's under the hood helps you appreciate why Cradle performs the way it does—and whether it will integrate smoothly with your existing infrastructure.

Cloud Infrastructure

Cradle is built on Google Cloud Platform with data centers located in the Netherlands (europe-west4 region), ensuring your data stays within the EU. This matters for regulatory compliance and data sovereignty requirements. The infrastructure is fully managed—you never need to worry about provisioning GPUs, managing model training pipelines, or maintaining servers. Cradle handles all of that, updating AI models every two weeks so you always benefit from the latest improvements.

Multi-Property Optimization Engine

The core optimization engine can handle any measurable protein attribute you want to improve. Whether it's enzymatic activity, thermal stability, binding kinetics, expression yield, or something more specialized, the system models how these properties relate to each other and finds candidates that meet all your targets simultaneously. This isn't a simple trade-off calculator—it uses sophisticated machine learning to understand complex relationships between sequence and function.

Modular Task System

When you need to explore multiple hypotheses in parallel, Cradle's modular task system lets you run several training and generation configurations simultaneously. This accelerates discovery by allowing your team to compare different approaches without sequential bottlenecks.

Wet Lab Verification

Here's something that distinguishes Cradle from purely computational tools: we maintain our own wet laboratory in Amsterdam where every platform feature gets tested before release. This means when Cradle generates a design, it's not just a computational prediction—it's been validated under real experimental conditions. Your team benefits from this verification without needing to run your own preliminary tests.

API-First Design

For teams with sophisticated automation needs, Cradle offers comprehensive API access covering the entire workflow. You can programmatically submit design requests, retrieve results, integrate with laboratory information management systems (LIMS), and build automated pipelines that combine AI design with high-throughput experimentation. This makes Cradle suitable for organizations looking to scale their protein engineering operations beyond manual workflows.

Continuous Learning

Unlike static software, Cradle improves continuously. Each time you upload experimental results, the models incorporate that feedback, becoming more accurate for your specific protein family and experimental context. This learning effect compounds over time—one of the most compelling reasons to adopt the platform early and build your proprietary dataset.

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Security and Compliance

If you're evaluating enterprise software for scientific R&D, security and intellectual property protection are likely top of mind. Here's exactly how Cradle handles these concerns.

Data Protection

Your data is encrypted both at rest (AES-256) and in transit (TLS 1.2+). Cradle maintains SOC 2 Type II certification and is fully GDPR compliant. Critically, your experimental data is never used to train models for other customers—each organization gets logically isolated model environments. Your data trains only your models.

Data Location

All customer data is stored in Google Cloud's Netherlands region (europe-west4), with automatic replication to other EU regions for redundancy. If your organization has specific data residency requirements, this EU-centric architecture addresses them directly.

Intellectual Property

You retain full ownership of all intellectual property generated through the platform. Cradle charges a software subscription fee only—there are no royalty obligations or IP licensing concerns. Your designs, your candidates, your breakthroughs: 100% yours.

Access Controls

The platform supports enterprise identity management through SSO integration with Google and Microsoft, plus multi-factor authentication (MFA) and passkey support. Role-based permissions let administrators control exactly what each team member can access, view, or modify.

Trust and Transparency

Cradle publishes a trust center with detailed security documentation, vulnerability reporting procedures, and clear policies. If your organization requires vendor security assessments, the team can provide supporting documentation and answer questions directly.

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Frequently Asked Questions