New Workflow Streamlines Protein Structural Analysis and Supports the Growing Role of AI in Drug Discovery

GenNext® Technologies, Inc., a pioneer in protein footprinting, is collaborating with Thermo Fisher Scientific, the world leader in serving science, to provide a simplified structural biology workflow designed to improve biotherapeutic development. The organizations are combining GenNext’s AutoFox® Protein Footprinting System with Thermo Fisher’s industry-leading liquid chromatography-mass spectrometry (LC-MS) solutions, particularly Thermo Scientific™ Orbitrap™ instrumentation, sample preparation technology and other structural proteomics consumables, such as crosslinkers and fluorescence labels, to create a powerful, end-to-end workflow solution for researchers working on complex protein structure and drug interaction studies.

The integrated workflow delivers high-resolution insights into protein structure and dynamics—essential for optimizing drug safety, efficacy and delivery. It also offers researchers a valuable toolset to help validate structural models generated by artificial intelligence (AI), an emerging frontier in drug discovery.

“We’re thrilled to collaborate with Thermo Fisher Scientific in advancing the boundaries of structural biology,” said Scot Weinberger, CEO, GenNext Technologies. “By integrating our Fox® product line with Thermo Fisher’s MS instrumentation such as Thermo Scientific™ Orbitrap™ Tribrid™ MS or Thermo Scientific™ Orbitrap Exploris™ MS, advanced reagents and data processing software, researchers can rapidly gain unprecedented visibility into biomolecular structure and behavior with unprecedented speed and simplicity.”

High-Resolution Insights, Simplified Workflow

The workflow begins with GenNext’s AutoFox® system, which uses Radical Protein Footprinting to map protein shape, flexibility and binding interactions in near-native conditions. This structural information is then captured with high sensitivity and precision using Thermo Fisher’s Orbitrap mass spectrometers, supported by EasyPep™ Sample Prep Kits and Tandem Mass Tag reagents to enhance consistency, enable replicate pooling and maximize protein coverage. Leveraging the Thermo Scientific™ Orbitrap™ Astral™ mass spectrometer further uplifts the workflow by providing fast throughput, high sensitivity and deep proteome coverage to expedite protein discovery and characterization.

Data is processed using GenNext’s FoxWare® Software and Thermo Scientific’s Proteome Discoverer software, creating a seamless workflow from sample preparation to analysis and interpretation. The result is a simplified yet robust solution for structural biology research, especially important for the development of biologics and biosimilars.

“Structural biology is foundational to the understanding of the molecular basis of biological activity and for the development of new therapeutic strategies,” said Pushkin Pant, Vice President and General Manager of Life Sciences Mass Spectrometry at Thermo Fisher Scientific. “Our collaboration with GenNext, enables scientists to generate deeper, more actionable insights through a synergistic technology approach.”

Supporting the Next Generation of Drug Discovery

While AI tools are accelerating drug discovery by predicting protein structures and drug interactions, these predictions require experimental validation to become useful. The GenNext–Thermo Fisher workflow supports this effort by enabling researchers to efficiently test and refine AI-generated models—an approach already successfully demonstrated by GenNext’s researchers and clients.

This ability to combine speed, precision and real-world validation positions the workflow as a powerful asset in both traditional and AI-enhanced drug development.

About GenNext Technologies

GenNext Technologies, Inc., develops instrumentation, software, and services that help scientists understand and optimize the structure and behavior of therapeutic proteins. The company’s patented protein footprinting technology enables faster, safer, and more reproducible structural analysis—empowering researchers to accelerate drug development and improve therapeutic outcomes.