Transforming Structural Biology Research with 3decision®: A customer success story
For structural biologists, providing and interpreting structural insights is essential to support rational drug design. However, 3D protein structures can originate from different experimental methods (such as cryo‑EM or X‑ray crystallography), include a wide range of molecular modalities (from small molecules to antibodies), and are accompanied by extensive metadata. As managing this information efficiently becomes increasingly challenging, many structural biologists face fragmented workflows, time-consuming manual steps, and limited opportunities for seamless collaboration across teams.
In this story, you will discover how Sanofi’s structural biologists addressed the challenges of 3D structural data management by implementing Discngine’s 3decision® – a comprehensive protein structure repository that centralizes all 3D protein structures and associated data within a single collaborative platform.
The article is based on insights from Dr. Alexey Rak, Head of Bio Structure and Biophysics at Sanofi, France.
Alexey Rak holds a Ph.D. in Biochemistry and Biophysics and previously served as a Team Leader at the Max Planck Institute in Germany before joining Sanofi in Paris in 2007. At Sanofi, he led the development of new methods for characterizing biomolecular interactions, advanced approaches for de novo structure determination, and established a cryo‑EM facility aligned with the field’s most advanced practices. Since 2014, he has led the Bio Structure and Biophysics department within Integrated Drug Discovery, overseeing and coordinating these activities across the organization agnostically to modalities and therapeutic areas
Persistent Challenges and Requirements for a Modern Solution
Structural biologists at Sanofi faced several challenges with their legacy in-house protein database, including:
Difficulties in maintaining and updating an internally developed system, which required ongoing effort to keep operational
Limited support for modern experimental methods — the platform handled only NMR and X‑ray structures and was not designed to accommodate data coming from new methods like cryo‑EM
Incomplete data coverage — it stored only internal structures and did not integrate publicly available Protein Data Bank entries
Siloed technology and fragmented data led to inefficiencies, leaving too little time for scientific interpretation. The goal was to allow scientists to streamline structural data management with a new approach.
“Before 3decision®, we used an older generation internally developed database that limited us in storing cryo-EM generated structural data and required frequent maintenance. Now, this powerful platform serves as our central hub for all structural biology data and as a tool for initial structure analysis, transforming how we approach drug discovery.”
When looking for a new solution, the primary requirement for structural biologists was centralization. The ideal solution needed to gather structures from multiple sources - both public and internal - and support multiple structure-determination methods such as X-ray crystallography and cryo-EM. The goal was to efficiently mine, visualize, and analyze all 3D structures without switching between multiple tools.
Instead of investing in another custom‑built application that would require ongoing hosting and maintenance, the team opted for a low‑maintenance, off‑the‑shelf SaaS solution. By choosing a ready-to-use cloud platform with no infrastructure to manage, they could eliminate the operational burden of supporting legacy tools while ensuring a scalable, sustainable system for structural data management.
After evaluating these needs and several solutions on the market, the team concluded that the 3decision® solution meets these requirements perfectly, while additionally offering tailored services and support.
Unified Structural Biology Data: How 3decision® Makes a Difference
With 3decision®, Sanofi’s structural biology team can now access all their structural data in one central place. The platform unifies X‑ray, NMR, and cryo‑EM data in a single searchable environment that brings together both internal structures and publicly available PDB entries. Its integrated 3D viewer adds advanced visualization capabilities that enhance the group’s analysis capabilities.
Thanks to cloud-based architecture and user-friendly UI, scientists can easily share structural insights across teams, supporting seamless communication throughout structure-guided drug design projects.
3decision® is also almost fully integrated with Sanofi's electronic lab notebook system and fully connected to the downstream analysis tools, reducing manual handoffs and ensuring data consistency.
Beyond the platform itself, users value the responsiveness of the Discngine support team. Sanofi also benefits from tailored services that adapt the solution as their needs evolve, ensuring the platform continues to support their scientific ambitions over time.
“As a result of implementing 3decision®, we improved efficiency, achieved better collaboration, and can now spend more time focusing on scientific interpretation rather than data wrangling.”
Conclusion
For structural biology experts, data is only as valuable as the insights it enables. The shift to 3decision® has provided a centralized environment that turns complex structural data into actionable knowledge, allowing scientists to focus on science, not data management.
The long-standing collaboration between Sanofi and Discngine has helped the structural biology group to overcome the limitations of traditional systems and fully leverage a cloud-based solution that now serves as a single source for all protein structures and related metadata.
The collaboration doesn’t stop here. Sanofi and Discngine continue working together to streamline workflows and strengthen the platform. The structural biology team is supported throughout the process — improving structure import, enhancing data quality, and advancing the integration of additional internal data, including sequence annotations for large‑molecule research. This ongoing partnership ensures that 3decision® evolves in step with Sanofi’s scientific needs.
“Our partnership with Discngine exemplifies how the right technology and collaboration can accelerate innovation. Looking forward to continuing this journey together as we push the boundaries of structural biology in drug discovery.”
