Paratope-PLUS^®

Display methods assess binding in a pooled competitive format and evaluate only one property at a time. Paratope-PLUS individually measures both binding and expression for each variant, providing parallel data for every single mutation. This comprehensive approach provides several advantages: 

• Multiplexed optimization: Paratope-PLUS provides data for optimization of multiple parameters at the same time, such as expression, binding affinity, species reactivity, and developability 

• Patent-ready resolution: Provides the residue-level resolution that is essential for meeting USPTO requirements for enablement and written description in antibody patent claims 

• Unbiased coverage: Avoids the selection bias inherent in display techniques 

• Works with challenging targets: Successfully handles complex or poorly expressing proteins that pose difficulties for display methods.  

Comprehensive CDR scanning (Paratope-PLUS) is one of many terms that describe systematic mutagenesis across antibody CDRs. Other terms include non-biased site saturation mutagenesis, CDR saturation mutagenesis, deep mutational CDR scanning, site-directed saturated mutagenesis, single-point saturation mutagenesis, and saturation scanning mutagenesis.  

What sets Paratope-PLUS apart is its ability to deliver a complete, high-throughput, single–amino acid resolution dataset that simultaneously supports robust patent protection and antibody engineering improvements across multiple parameters.

Paratope-PLUS and structural techniques provide complementary insights. Methods like Cryo-EM or X-ray crystallography define the physical contact footprint between antibody and antigen. Paratope-PLUS identifies the energetically critical residues required for binding and all substitutions that maintain or improve binding. In most cases, the critical residues we identify overlap with the footprint. Importantly, we also detect critical residues outside the direct binding interface that impact function— insights often missed by structural methods alone.  

Our platform builds on 20+ years of protein engineering using the same proven principles as epitope mapping, validated across 2,000+ antibodies and included in 100+ publications and patents. 

Paratope-PLUS is the only approach that generates the complete experimental dataset required to support fully enabled genus claims. It supports USPTO requirements for both enablement and written description. And the final report includes draft patent claims, giving your patent attorneys a head start in translating your data into actionable patent language.  

For a comparison with other antibody patent strategies, see Banik et al., 2025 (PDF), Table 3.

To initiate a Paratope-PLUS CDR-Scanning project, you’ll need to provide the antibody’s CDR sequences and specify which regions to scan (e.g., all six CDRs or only the heavy chain). We’ll also ask you to complete a project setup form so we can understand how the antibody has been expressed and tested, including formats, expression systems, and whether it’s been used in ELISA. Integral Molecular covers recombinant antigen sourcing costs up to a specified amount. Any additional antigen expenses are passed through at cost, with prior approval.

Plasmid clones and purified antibody protein are not standard Paratope-PLUS deliverables—but we can provide them through separate services. To maintain affordability, our libraries are cloned in a proprietary vector system optimized for high-throughput screening, and we produce the plasmid and protein quantities necessary for only the screen itself. However, Integral Molecular offers follow-up services for variant re–cloning into your preferred vector system, and protein expression and purification of selected variants.

We typically identify single-residue substitutions that individually improve binding affinity 2– to 4-fold, consistent with published literature. Combinations of these mutations, which can be tested as an optional component of the project, can result in improvements of 5- to 10-fold. Beyond affinity maturation, Paratope-PLUS also identifies substitutions that enhance expression levels, developability properties, and species cross-reactivity.

Paratope-PLUS uses high-throughput periprep expression and screening in E. coli—the same system used successfully in phage display for decades. This approach enables:  

• Cost efficiency: Comprehensive datasets at a significantly lower cost than mammalian expression systems   

• Proven reliability: Validated technology with decades of successful application 

• High-resolution data: Complete binding and expression information for every variant 

This cost-effectiveness translates directly into customer value without compromising data quality for patent protection and antibody engineering decisions.

Yes, we store the libraries for up to a year, allowing you to conduct additional screening experiments without the time or expense of library creation. This allows you to test against additional targets or antigens, perform follow-up validation studies, and explore different binding conditions.