GHP Magazine is proud to announce that Bio-Prodict has been awarded for its second consecutive year in the 2026 Global Excellence Awards, recognised as the Best Global Mutation Prediction Company 2026. This recognition follows the groundbreaking launch of the company’s 3DM Engineering AI platform, which has redefined the boundaries of protein design and mutation prediction. In light of Bio-Prodict’s significant success, we sat down with Founder and CCO Henk-Jan Joosten to find out more.
Based in Nijmegen, the Netherlands, Bio-Prodict is a private company specialising in software design, structured biology, and protein analysis. Since its inception in 2008, the company has risen to emerge as a pioneer in the field of protein R&D, playing an instrumental role in reshaping the ways in which scientists and researchers understand and manipulate proteins.
The cornerstone of Bio-Prodict’s success lies in the company’s proprietary 3DM databases. 3DM protein family databases consist of many different types of data, such as sequences, structures, 3D alignments, literature, patent, ligand binding, SNP data, mutation data, and more. Bio-Prodict has created 3DM databases for all available protein families, positioning itself at the forefront of the industry with the largest highly organised protein dataset in the world.
What’s more, this data is all synchronised within 3DM via a renumbering of all sequences and all structures based on a 3D alignment. A unique introduction, the 3D numbering scheme hyperlinks all data to enable its transfer between homologues proteins. This synchronisation has proven effective, facilitating the diagnosis of a patient with HYPP with a mutation that had not been observed in humans before.
Where doctors could not confirm the mutation to be the cause, 3DM was able to provide evidence of a running horse that had died of this same condition. The numbering of both the human and horse proteins are synchronised within 3DM, and the mutations shared the same 3D numbers, allowing for a diagnosis that would not have been possible without these groundbreaking databases.
By synchronising and structuring vast amounts of protein data across all known families, Bio-Prodict has created the ultimate training ground for artificial intelligence. After years of training within these databases, Bio-Prodict released 3DM Engineering in November 2024. 3DM Engineering is an AI platform designed to generally “understand” how proteins function, and can predict the effects of mutations, as well as which can be combined. Its ability to accurately predict higher-order mutants makes this platform so valuable, as such combinations cannot be predicted by rational design.
“Unlike generic models, 3DM Engineering is built upon more than 100,000 of Bio-Prodict’s high-quality, family-specific datasets, allowing it to uncover hidden correlations buried deep within complex biological systems,” Henk-Jan Joosten commented. “The results we have seen from 3DM Engineering are, quite simply, transformative.”
“The results we have seen from 3DM Engineering are, quite simply, transformative.”
While many in the industry are still exploring the potential of artificial intelligence, Bio-Prodict is already delivering results that surpass traditional high-throughput screening methods in both speed and accuracy. Since its release, 3DM Engineering has been utilised by seven of the top ten global pharmaceutical companies, in addition to numerous biotech leaders. Its ability to predict highly complex mutants, often containing five simultaneous mutations, allows researchers to achieve what would previously require multiple rounds of exhaustive laboratory screening in a single round of just 20-50 variants.
A recent study has highlighted the platform’s ability to go beyond current state-of-the-art capabilities. In a project involving an enzyme that had reached a plateau after 30 rounds of high throughput protein engineering, 3DM Engineering succeeded where high throughputs of ten-thousands of variants could not. By predicting just 46 mutants, each with five mutations, the 3DM Engineering identified nine mutants with increased activity, including one with a staggering 40% improvement.
Remarkably, these quintuple mutants featured fundamentally different amino acid compositions, demonstrating that 3DM Engineering systematically uncovers distinct functional peaks within the sequence-activity landscape, surpassing the performance plateau of traditional high-throughput laboratory methods.
From enhancing protein stability, enzyme activity, and changing enzyme enantioselectivity to accelerating drug design and DNA diagnostics, Bio-Prodict’s AI-driven approach is proving that the future of R&D lies in the synergy of structured laboratory data and intelligent prediction. GHP Magazine is honoured to recognise Bio-Prodict for a second consecutive year, applauding the company for its visionary contribution to the life sciences sector and its role in shaping the future of protein engineering.
Contact Details
Contact: Henk-Jan Joosten
Company: Bio-Prodict BV
Web Address: www.bio-prodict.com
