Structural target
The target surface, or epitopes on it, provides the reference for generating, positioning and evaluating binder candidates.
AI-Driven Protein Design Platform
Intelligent protein design.
Faster innovation.
AI-driven protein design for more stable proteins that are easier to produce.
We combine bioinformatics, structural biology, physics-based modeling and modern AI methods in protein design to engineer optimized molecules. This helps increase the probability of success in our customers' development projects, shorten development timelines and make the process more efficient and cost-effective.
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In silico methodology
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Years scientific experience
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Data-driven insights
Network · Collaborations · Scientific Environment
Our Services
Three pillars of computational biotech
ProtoVela combines decades of scientific experience and expertise in structural biology and bioinformatics with modern in silico methods and artificial intelligence — delivering tangible results without the time and cost burden of a wet lab for sequence optimization.
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Structure-based protein design for next-generation proteins
Targeted optimization of stability, expression and biophysical properties.
ProtoVela uses modern in silico methods and structure-based design to optimize protein sequences for higher stability, improved expression and optimal biophysical properties. This yields better-performing proteins while efficiently accelerating our customers’ process development.
Service · 01
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AI-driven protein design for miniprotein development
Tailored binders for defined target-protein surfaces.
Using advanced AI-driven methods, ProtoVela develops tailored miniproteins with high affinity and specificity for defined surface structures on target proteins. These compact, purpose-designed proteins offer an innovative alternative to conventional antibodies and open new possibilities in biotechnology, diagnostics and therapeutics.
Service · 02
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Bioinformatics & structural biology — insights into protein structure, dynamics and function
Integrated analyses from sequence and structure to dynamics and function.
Comprehensive bioinformatic analyses of customer proteins, physics- and AI-based structure modeling, and mutation and stability analyses of peptides, soluble proteins, membrane proteins and biomolecular complexes are complemented by analyses of conformational spaces, protein dynamics and structural states. This provides detailed insight into structure–function relationships and molecular properties.
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Computational-to-experimental workflow
From the structural target to a prioritized candidate series
Computational design reduces the search space, prioritizes promising candidates and prepares focused experimental validation in collaboration with Trenzyme.
Active pipelineBinder design
Pipeline for binder generation and testing
From the structural target through binder generation and optimization to experimental binding characterization by ITC.
Optimized binder candidates with a clear testing strategyITC characterization of selected candidates
Defined target surface
The target surface, or epitopes on it, provides the reference for generating, positioning and evaluating binder candidates.
Reference Project · Scientific Leadership
Hydrolase design — 16 days, seven winners
An anonymized example from industrial protein-design work: a design approach now used at ProtoVela was applied to a hydrolase scaffold and yielded expressed variants with improved stability for seven of the eight selected sequences.
Project from the earlier industrial work of ProtoVela’s scientific director, Dr. Kornelius Zeth. The underlying design methodology is now used at ProtoVela.
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7 / 8
designs expressed
Seven of the eight selected sequences were successfully expressed in the host system.
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+18 °C
higher melting point
The top design increased Tm from 55 °C to 73 °C — an 18 °C increase.
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2.7×
expression yield
The best variant achieved up to 2.7 times the parent’s expression yield.
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16 days
design turnaround
From client sequence to delivered, ranked sequence set.
Fig.02— Biomolecule
About ProtoVela
Pioneers in biotechnology and protein design
ProtoVela is an emerging biotechnology startup with deep expertise in protein structures, structure-based protein design, and bioinformatics.
We favor rational protein design over directed evolution, leveraging advanced in silico approaches to improve protein stability, expression, and handling. Our methods are built on years of scientific experience and are designed to deliver tangible results that can be validated by our partners in experimental environments.
What to expect
What does modern protein design actually deliver?
Classical directed evolution often meant screening hundreds of thousands of variants. With AI-driven design, a few dozen carefully selected candidates are usually enough to reach comparable or better results.
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~40 vs 100k
Variants to screen
Directed evolution used to require screening in the range of 100,000 variants. Modern AI-driven design typically narrows this to a few dozen carefully chosen sequences that actually go into expression.
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2–3×
Expression yield
Optimized sequences routinely reach two to three times the recombinant expression yield of the parent sequence in typical projects.
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10–100×
Activity gain
For enzymes and functional proteins, activity improvements of 10× to 100× are realistic — depending on target profile and starting protein.
Indicative ranges from project experience · results depend on system and target profile
Free intro call & Project Assessment
Assess first, then engineer — at no upfront cost.
Send us a non-confidential summary of your goal. After agreeing an NDA and secure data-transfer route where needed, we assess which optimization goals are realistic, how to prioritize them and what a fine-tuning project would look like. Only then do you decide whether to commission a paid engagement.
- Free intro call with our scientific leadership.
- Free project assessment — with secure sequence exchange after initial contact.
- Clear go / no-go recommendation with realistic expectations.
- Only the subsequent fine-tuning work is paid.
FAQ
Frequently asked questions
Quick answers about ProtoVela's protein engineering services, methods and partnerships.
Rational protein design uses structural and computational insight to engineer specific changes in a protein, while directed evolution relies on random mutation and screening. ProtoVela focuses on rational protein design powered by physics-based modeling and generative AI, which is faster, cheaper and produces IP-clean candidates without wet lab cycles.
Yes. Membrane protein structure prediction is a core specialty — including VDAC structural analysis and other challenging transporters where AlphaFold2 limitations are well documented. We combine physics-based protein modeling with curated structural data to deliver reliable models.
You do. ProtoVela works on a clear, contract-based IP ownership model: all generative protein design outputs delivered to a client are owned by the client. We do not retain shared rights to the designs.
Yes. We support biotech spin-offs and pharma teams as an embedded computational partner — from feasibility studies and target triage to long-term co-development of an AI-driven protein engineering platform.
De novo miniprotein therapeutics and antimicrobial peptide drug discovery — including overcoming bacterial efflux pumps with AMPs — are active focus areas, directly informed by Dr. Zeth's published research on membrane proteins.
ProtoVela UG is a protein engineering startup based in Regensburg, Bavaria, Germany, working with partners across Europe and globally.
Blog
Updates from research and practice.
Developments in structural biology, AI-assisted protein design and biotech ecosystems.
Protein Engineering & AI
From AlphaFold to Protein Design: Why the 2024 Nobel Prize Matters for Biotech
The 2024 Nobel Prize in Chemistry marked a turning point: computational protein design and protein structure prediction have become central technologies for modern biotech innovation.
5 minRead more →
Protein Engineering & AI
Directed Evolution and Rational Design: Two Complementary Paths to Better Proteins
Directed evolution and rational design are often framed as competing paradigms. In practice, strong protein engineering programs combine both.
4 minRead more →
Structural Biology
Seeing Biomolecules: Why Structural Biology Became a Strategic Biotech Capability
Cryo-EM, X-ray crystallography, NMR, mass spectrometry and computational modeling form the analytical backbone of structure-informed innovation.
4 minRead more →
Keep reading · Sitemap
Explore further
Services, scientific evidence, team expertise and a direct path to project assessment.
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Expertise
Services, molecule classes and scientific application areas in detail.
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Why ProtoVela
Principles, optimisation targets and the eight-step design process.
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About
Team, location and scientific leadership behind ProtoVela.
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Blog
Field notes on AI, structural biology and protein design.
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Contact
Book a free intro call and Project Assessment.