Investigate individual interaction partners
When one protein interacts with several partners, a knockout can make their contributions difficult to distinguish. We design binders as tools to help test the role of a particular interaction.
CUSTOM PROTEIN DESIGN
Protein binders,
designed for
the site you choose.
Block a protein interaction to investigate what it does. FoldArc designs binders for selected sites on your target and delivers sequences and computational evaluations for experimental testing.
You can start the conversation before choosing a binding site.
DESIGN AT THE INTERFACE01 / PD-L1
DESIGN
Start with the interaction to inhibit
DELIVERY
RESEARCH10 sequences and evaluationsStandard scope
Published methods and binding results ↗
EXPLORE PROTEIN INTERACTIONS
A tool to study
a specific molecular function.
Binders are small proteins that attach to a target’s surface.
We design them to bind an interaction interface, with the aim of blocking a specific protein interaction.
Target the interface you want to inhibit
For interactions that are difficult to study with existing inhibitors, we assess possible binding sites using the target structure and information about its partner, then select candidates for experimental testing.
START WITH YOUR RESEARCH QUESTION
Which interaction do you want to block, and what will you measure?
We discuss your objective and experimental system to choose a binding site together. Our standard deliverables are designed sequences and computational evaluations. Binding and effects on the interaction or function are then tested in your experiments.
OUR DESIGN METHOD
Refine the sequence.
Preserve the binding pose.
We combine generation, sequence optimization, and evaluation with multiple structure prediction models to select candidates for experiments.
- 01 / GENERATE
Choose a site and generate candidates
We consider your target structure and research objective, then use multiple generative models to produce approximately 10,000 candidate designs as a starting point.
- 02 / OPTIMIZE
Optimize while retaining the pose
Our ArcRefine method passes structural information between prediction steps to refine sequences while preserving the original binding pose.
- 03 / EVALUATE
Select with multiple models
We assess predicted binding modes and confidence using multiple structure prediction models, then deliver selected sequences with their computational evaluations.
EXPERIMENTAL EVIDENCE
Binding measured
by an independent lab.
Adaptyv Bio evaluated 40 submitted designs by biolayer interferometry (BLI): 10 from each unoptimized and optimized group for PD-L1 and TNFα.
Read the research overview ↗BINDING-POSITIVE / SUBMITTED DESIGNS
TNFα
Unoptimized1 / 10
Optimized6 / 10
PD-L1
Unoptimized1 / 10
Optimized4 / 10
The groups were independently selected and compare the complete design workflows. These results demonstrate binding, not cellular inhibition or a success rate for new targets.
PUBLICATION · 2026Read the paper ↗
ArcRefine improves de novo binder designs while preserving binding modes
Ken Osumi · Preprint (not peer reviewed) · DOI: 10.5281/zenodo.23115832WHAT YOU RECEIVE
10 sequences.
Computational evaluations.
Ready for you to test.
Selected for your target and application,
delivered as electronic data for your lab.
This is the standard scope. Sequence count and deliverables are agreed for each project.
01
Amino acid and DNA sequences
We discuss tags, fusion domains, species, and other requirements during design.
02
Evaluations for each design
Predicted binding poses and computational metrics help you choose candidates for experiments.
OPTION
Synthesis and experimental services
Gene synthesis, plasmid delivery, and outsourced protein production or binding measurements can be arranged under a separate scope and quotation.
HOW WE WORK
Assess feasibility
before committing.
Review the initial design results and quotation before deciding whether to proceed with a full project.
- 01
FREE · ABOUT 1 WEEK
Discuss and test
We discuss your target, research question, and experimental system, then assess binding sites and computational feasibility.
- 02
REVIEW BEFORE YOU DECIDE
Results and quotation
We present the feasibility results, proposed deliverables, and cost. You decide whether to commission the full design.
- 03
ABOUT 2 WEEKS AFTER ORDER
Design and delivery
We generate, optimize, and select candidates, then deliver sequences and evaluations. Further design work can be discussed in light of experimental results.
Timelines are estimates. Synthesis and outsourced assays require additional scheduling. Expression, binding, and function are tested in your experimental system after delivery.
USING YOUR DESIGNS
From delivered sequences
to your experiments.
Typical uses after receiving the sequences.
Gene delivery and protein production or purification are carried out by your lab or your service provider.
For intracellular targets
Introduce the gene→Express in cells
Introduce a gene encoding the binder. Choose a promoter for the desired expression conditions and use tags to assess expression and localization.
For extracellular or cell-surface targets
Purify the protein→Add to your assay
Add the produced and purified binder to your experimental system and vary its concentration to assess binding or activity.
Typical designs are around 100 amino acids and 10–20 kDa. Gene synthesis, plasmid delivery, or production and assay arrangements are discussed separately if needed.
OTHER APPLICATIONS
Detection and structural studies, too.
Alongside interaction inhibition, we can discuss binder designs for these applications.
Detection probes
To investigate the presence or localization of a target. We design binding probes with your detection site, tags, and assay in mind.
Cryo-EM stabilizers and fiducial markers
To help stabilize a state of interest or provide a marker for identifying particle position and orientation. We assess binding sites in the context of your target structure and the state you want to observe.
Detection performance and stabilization effects require application-specific experimental evaluation.
QUESTIONS
Frequently asked questions
Can I contact you before choosing a binding site?
Yes. Start with your target, the function you want to investigate, and any known interaction partners. We use available structures and structure predictions to assess possible sites and computational feasibility.
Am I buying an existing, validated binder?
This is a custom design service. We design new binders for your target and research objective. You can review a free feasibility design and a quotation before deciding whether to commission the full project.
Who tests binding and function?
The standard deliverables are sequences and computational evaluations. Expression, binding, and the intended function are tested in your experimental system. Computational assessments do not guarantee experimental binding or activity. Outsourced protein production or binding measurements can be discussed as a separate scope.
What will I receive?
Amino acid and DNA sequences, together with computational evaluations for each design, are delivered electronically. Gene synthesis and plasmid delivery are available by arrangement. Tags, fusion domains, and species requirements can be discussed during design.
When will I know the cost?
We provide a quotation and a proposed scope with the feasibility results. Cost depends on the target, binding site, selectivity requirements, and delivery format. The initial feasibility design is free, with no obligation to proceed.
SERVICE GUIDE
Explore the service.
Start with the guide.
Learn about applications, experimental results, and how a project works. Download the English PDF immediately after submitting the form.
- 01Designing for interaction inhibition and experimental use
- 02Design methods and independent binding measurements
- 03Deliverables, a free feasibility design, and project steps