Removing barriers: academia and industry collaborate to open commercial access to protein design software

A collaborative effort from academia and industry has made a popular protein design software package free for commercial use. All previously restricted components have now been replaced, removing a significant barrier for biotechnology companies wanting to use the pipeline.

 Making AI-powered protein design more accessible

Tools such as AlphaFold2 and RFDiffusion have dramatically expanded researchers’ ability to predict and design protein structures, opening new possibilities for engineering proteins with useful biological functions. However, taking full advantage of these new tools can still present significant technical barriers.

ProteinDJ was developed to make these powerful methods easier to use.

Contributors for the ProteinDJ V3.0 release: WEHI. Australian BioCommons, UNSW Sydney, and Audax

Originally developed and published by Dylan Silke, Dr Josh Hardy and Prof Isabelle Lucet, from the Papenfuss and Lucet laboratories at WEHI, ProteinDJ streamlines the protein binder design process into a single, modular workflow that is easy to install, efficient to run and flexible enough to incorporate new methods as the field evolves. It guides the user through four key stages: designing a binder’s shape (fold), generating an amino acid sequence for it, predicting a 3D structure and analysing the results.

While ProteinDJ itself is open source, some of the software components it relied upon carried licences that restricted how the workflow could be used and distributed. These restrictions presented practical barriers to broader adoption, particularly within biotechnology companies. Dr Josh Hardy (WEHI), Dr David Ladd (Audax), and Dr Thomas Litfin (Australian BioCommons/UNSW) have now worked together to remove these barriers alongside a range of other improvements as part of the release of ProteinDJ version 3.0. 

From webinar to collaboration and national capability

As part of the Leveraging deep learning to design custom protein-binding proteins webinar series developed by the Australian Structural Biology Computing community, Australian BioCommons hosted a ProteinDJ webinar in late 2025. The popular presentation was seen by researchers at the Australian biotechnology company, Audax, who are developing targeted immunotherapies for oncology and autoimmune diseases. Identifying the potential of the ProteinDJ pipeline, they began work to replace the licensed dependencies. Simultaneously, the Australian BioCommons had been working with the ProteinDJ developer, Dr Josh Hardy, to address the license restrictions. In mid-2026, the groups joined forces and began working collaboratively to merge and validate the new components alongside several performance and usability improvements. 

This work paves the way for ProteinDJ to be incorporated into the Australian BioCommons Structural Biology Platform, which is currently being developed with the research community, and will soon become available for Australian researchers to run AI-based structural biology workflows.

Check out ProteinDJ on GitHub

Read the publication - ProteinDJ: A high-performance and modular protein design pipeline

View the ProteinDJ webinar recording