A Merck KGaA, Darmstadt, Germany Digital Chemistry Solution

We engineer your proteins.

De novo protein design and protein optimization. Work with our protein design and optimization experts, from first brief to validated leads with results.

Proven Impact

across binder design, affinity optimization, and enzyme engineering

3 weeks

binding confirmed in internal work

Optimization

well-established Bayesian optimization platform BayBE, developed in-house

Domain Expertise

>350 years in Life Science, ISO 13485-certified manufacturing via MilliporeSigma

Our Services

What do you need?

Three services. Choose the one that fits your project, or combine them for end-to-end coverage.

Binder Design

You have a target. You need binders that bind to it.

  • De novo design from target structure
  • Nanobodies, miniproteins, or custom scaffolds
  • Optional: wet-lab validation included

Binder Optimization

You have binders. You need them better.

  • Bring your own lead candidates
  • BayBE-driven multi-parameter optimization
  • Per-round booking: Stop when you’re satisfied
  • Wet-lab validation in each round

Protein Optimization

You have an enzyme to improve. We design the campaign.

  • Bring your lead enzyme sequence
  • No prior assay data needed to start
  • Additional measurement data welcome
  • Enzymatic activity, stability, solubility, expression

Combine services: Book binder design and optimization together for end-to-end campaigns from target to development candidate. Or bring your own leads and book just optimization rounds.

Why Work With Us

We engineer for products, not just the assay.

A hit binds in an assay. A product is stable, expressible, and ready for the next stage of development. We optimize for products.

Proven track record

A validated history of designing functional binders across diverse target classes, including deliveries to EMD Serono for therapeutic development programs.

End-to-end service

A validated history of designing functional binders across diverse target classes, including deliveries to EMD Serono for therapeutic development programs.

Model-agnostic pipeline

We plug in the best generation model for your target: RFdiffusion, BindCraft, Boltz, ProteinMPNN. No vendor lock-in. Always the right approach.

BayBE optimization

Bayesian experimental design reduces cycles and maximizes information gain per wet-lab run. Used in our pipeline and trusted by NASA. Learn more about BayBE.

Proven Impact

Real projects, real proteins.

Eight campaigns from our design and optimization work.

From “Undruggable” to Multi-Epitope Hits

We delivered confirmed hits across two epitopes on a target that had no binding pocket and no prior art. All leads are under active development.

Reaching up t 87% Binder Success Rate

Systematic model selection across BindCraft, BoltzGen, and Proteina Complexa drove hit rates to 87% in a single campaign run.

Picomolar Affinity, Gold-Standard Proven

0.9 nM affinity confirmed by full BLI kinetic analysis: real association and dissociation rates, clean saturation, no artefact signatures.

Better Numbers are Easy. Better Products Are the Goal.

Affinity gain with simultaneously keeping specificity. Single-metric optimization would have picked different, worse candidates.

Precision Enzyme Engineering: 1000x Selectivity Gain

Structure-guided redesign cut the side reaction 1000-fold while preserving full target activity.

Fewer Experiments, Better Leads: Powered by BayBE

BayBE calculates the next best experiment at each cycle, cutting the wet-lab rounds needed to reach a target property profile.

Production Costs Reduced to a Fraction

We built thermostability and expression efficiency into the single scaffold from the start. Single-step purification was sufficient, cutting production and storage costs sharply.

Benchmark-Beating Upgrades

Our published sequence scanning workflow outperforms AlphaFold3, Protenix and Boltz on antibody-antigen and molecular glue predictions, two of the hardest classes for pharma.

Experimental Proof

What we can already show from internal work.

These are the strongest public signals we can share today. They come from assay-linked internal results and observed program outcomes, not market-size slides or cost promises.

Binding in 3 weeks

Internal work has already confirmed binding on a 3-week timeline.

Multiple hits from one plate

One internal de novo run produced multiple hits from a single design plate.

~15 nM internal example*

One internal example reached an estimated affinity around ~15 nM from early BLI data.

  • Lead candidates have already been confirmed by SPR, BLI, and ELISA workflows.
  • Optimization cycles can run in 4-6 weeks.
  • Our services are already being used across both de novo design and optimization work.

* Estimated from 3-point BLI in one internal example. Orthogonal follow-up was still ongoing at the time of the deck.

How It Works & Packages

Choose the engagement that fits your program.

Binder projects are turnkey — we handle everything from design to validation. Protein optimization is collaborative — you stay in the loop for testing.

» Binder Design & Optimization » Enzyme Optimization

Binding Design & Optimization

Turnkey from target brief to validated leads.

We run the full binder campaign for you: target analysis, de novo design, wet-lab confirmation, and optional BayBE-guided optimization rounds when you want to push affinity, stability, or developability further.

01

Target Analysis

We assess your target structure, identify binding hotspots and epitopes, and evaluate campaign feasibility before committing resources.

02

Computational Design

Our pipeline generates thousands of candidate binders using the best-suited generation model for your specific target and requirements.

03

Intelligent Filtering

Multi-objective scoring ranks candidates across affinity, stability, and developability. BayBE-driven Bayesian optimization explores the design space efficiently.

04

Structural Validation

Top candidates undergo structure prediction via AlphaFold2 and Boltz-2 to confirm binding pose geometry and interface quality.

05

Experimental Validation

We produce and characterize top designs by BLI. Additional assays available: SPR, ELISA, DSF, SEC.

06

Optimization & Delivery

Optional BayBE-guided optimization rounds improve affinity, stability, or developability. You receive validated sequences, binding data, and a full campaign report. Manufacturing via MilliporeSigma available.

Flexible entry: Already have lead binders? Skip to step 05 or 06 — book optimization rounds directly without a full design campaign.

Package Options

Start with computational design, add experimental confirmation, or bring existing leads straight into optimization rounds.

Design Only

Computational binder generation

from $5k

  • De novo binder design campaign
  • Ranked candidate sequences
  • Structural models for top hits
  • Full design campaign report

Design + Validation

Design through validated hits

from $25k

  • Everything in Design Only plus:
  • Wetlab binding validation (BLI / SPR / ELISA)
  • 100% Binder Guarantee
  • No payment if no binder delivered

Optimization Rounds

Improve your existing binders

from $15k/round

  • Bring your own lead binders
  • BayBE-guided multi-parameter optimization
  • Wet-lab validation each round
  • Book one round or several
  • Also available after a Design campaign

~2 weeks

Design only

~6 weeks

Design + Validation Fast Track

2–3 months

Design + Validation Standard

4–6 weeks

Per Optimization Round

Enzyme Optimization

Collaborative cycles built around your assay data.

You bring lead sequences and measured results. We train sequence-to-assay models, propose the next set of variants, and refine the campaign with you cycle by cycle.

01

You provide the data

Share your lead sequences and a dataset of sequence–property pairs. The more data points, the better our models perform. We assess feasibility and propose a campaign plan

02

We train & propose

We build sequence-to-property models on your data and use BayBE to propose the next round of variants — maximizing information gain and predicted improvement.

03

You test

You synthesize and assay the proposed variants in your own lab or through your preferred vendor. You own the testing workflow.

04

Iterate

Feed results back. We retrain models and propose the next round. Each cycle sharpens predictions. Continue until your target property threshold is met.

What this covers: Enzymatic activity, thermal stability, solubility, expression level, substrate specificity — any measurable protein property you can feed back as data.

Optimization Engagement

Collaborative variant design from your data

Custom /  per cycle · 1 week turnaround on our side

What You Provide

  • Lead enzyme sequences
  • Sequence-to-assay dataset (measured values)
  • Target activity or selectivity threshold

What We Deliver

  • Lead enzyme sequences
  • Sequence-to-assay dataset (measured values)
  • Target activity or selectivity threshold

How We Compare

Most services stop at computational candidates. We deliver validated, manufacturing-ready molecules.

Approach Design Validation Manufacturing Risk
Build in-house Requires hiring specialists You manage Separate vendor High: long ramp-up, uncertain output
Academic collaboration Best-effort, publication-driven Limited Not included High: timelines and IP unclear
Pure-compute CRO Generate candidates only Not included Not included Medium: no guarantee they bind
Traditional CRO Phage/yeast display Included Separate vendor Medium: slow, limited diversity
MilliporeSigma AI-driven, model-agnostic pipeline Included, BayBE-optimized MilliporeSigma integrated Low: guaranteed binders, end-to-end

Capabilities

Built to design binders and improve enzymes

» Binder Formats » Optimization Targets » Application Areas

Binding Formats

Flexible scaffolds for difficult biology.

Choose the architecture that fits your epitope geometry, delivery constraints, and downstream development path.

Nanobodies (VHH)

Single-domain antibody fragments. Compact ~15 kDa, thermostable, and versatile across challenging targets including GPCRs and intracellular proteins.

Miniproteins

Ultra-compact binders at 60-160 amino acids, engineered for maximum stability. Ideal for geometrically constrained epitopes.

Custom Scaffolds

Target-specific designs when standard formats don’t fit. Repeat proteins, cystine knots, and novel topologies guided by your epitope requirements.

Optimization Targets

From affinity to enzyme performance.

Run binder or enzyme campaigns around the properties that matter most for your program.

Binding Affinity

Drive Kd from micromolar to picomolar across binder design and optimization.

Enzymatic activity

Improve kcat, Km, or specificity for industrial and therapeutic enzymes.

Thermal Stability

Raise Tm for storage, formulation, and harsh operating conditions.

Solubility & Expression

Reduce aggregation and improve titers for manufacturing readiness.

Selectivity

Sharpen specificity to discriminate targets from close homologues.

Multi-Parameter

Optimize multiple properties simultaneously with Pareto-aware BayBE campaigns.

Application Areas

Where we deliver.

The same design and optimization stack adapts across therapeutics, tools, sensors, and industrial protein programs.

Therapeutic binders

Novel biologics for oncology, immunology, and rare disease targets.

Diagnostic Reagents

High-specificity capture molecules for clinical and point-of-care assays.

Industrial Enzymes

Engineered for activity, stability, and process compatibility at scale.

Research Tools

Affinity reagents, intrabodies, and molecular probes for basic research.

Biosensors

Recognition elements for electrochemical, optical, and lateral-flow platforms.

PPI Modulators

Disrupt or stabilize protein-protein interactions with precision-designed interfaces.

Get Started

You have proteins to engineer.

Whether you need binders designed from scratch, existing leads optimized, or protein properties improved — we are the computational partner to get you there.

  • You submit your inquiry
  • Feasibility assessment within 1 week
  • Campaign proposal with scope and quote
  • Approval: work begins
  • Results delivered

Design + Validation and Optimization packages include experimental binding readouts on top candidates.

Resources

Explore our latest white papers, webinars, and more to stay informed about cutting-edge advancements in AI-powered drug discovery and retrosynthesis.

Webinars

From Predictive Retrosynthesis to Real-World Routes: Connecting Digital Chemistry Workflows

Webinars Chemical Synthesis Drug Discovery

Videos

From Possibility to Probability: Accelerating Drug Discovery in the Lab of the Future [CES 2026]

Discover how to apply generative AI methods in hit identification, hit-to-lead, and lead optimization of novel molecules.

Videos Chemical Synthesis Drug Discovery

White Papers

Generative AI for Medicinal Chemistry Workflows

Learn how to unlock new chemical space with generative AI methods that expand options for drug discovery.

Featured White Papers Drug Discovery

News & Events

Stay up to date with recent news articles and upcoming conferences where you can connect with our experts.