Other features for v2 include template-guidance for #Boltz-2 prediction, auto-contig generation for #RFdiffusion, and models for #HyperMPNN. We have also made bug fixes, improvements to documentation, container updates and more. Details here: github.com/PapenfussLab/proteindj/releases/tag/v2.0.0

A big shoutout to @martinpacesa.bsky.social and team for creating a fantastic open-source package for binder design. You can read more about BindCraft here www.nature.com/articles/s41....

BindCraft is a standalone binder design pipeline (github.com/martinpacesa/BindCraft), but we have integrated only the first step of the BindCraft workflow (binder hallucination) in ProteinDJ. This is to utilise our existing downstream sequence design/structure prediction packages.

And thanks to Lyn Deng for creating such a cool ProteinDJ logo!

Special thanks to everyone who helped develop this software over the last year: Dylan Silke, Julie Iskander, Junqi Pan, Andrew Thompson, Tony Papenfuss and Isabelle Lucet. This was an interdisciplinary collaboration between the #PapenfussLab & #LucetLab at WEHI @wehi-research.bsky.social (5/5)

We also created Bindsweeper—a new tool to help you identify the optimal binder design parameters for your target protein. Bindsweeper enables the execution of multiple ProteinDJ runs to test different parameter combinations and reports success rates for each permutation. (4/5)

There are multiple ways you can use ProteinDJ for protein design. We have documentation and examples of different protein design applications, including de novo design, fold conditioning, partial diffusion, and motif scaffolding. There are also filters and metrics to help select designs (3/5)

ProteinDJ was designed for large-scale design campaigns and automatically batches designs over GPUs. It is highly portable and easy to install, with software containers for rapid deployment on HPC and workstation environments using Apptainer and Nextflow. github.com/PapenfussLab... (2/5)

And congratulations to Dylan for winning a poster prize!