@joshuamhardy.bsky.social
Structural biologist in Aus @WEHI. Cryo-electron microscopy of viruses and protein complexes #cryo-EM. Co-creator of ProteinDJ (He/Him)
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
25.11.2025 03:00 — 👍 0 🔁 0 💬 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....
25.11.2025 03:00 — 👍 1 🔁 0 💬 1 📌 0
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.
25.11.2025 03:00 — 👍 0 🔁 0 💬 1 📌 0
I am pleased to announce the release of ProteinDJ v2! This is a major update that integrates BindCraft into the pipeline as an alternative to RFdiffusion for binder generation. You can try it out here: github.com/PapenfussLab/proteindj
#ProteinDJ #BindCraft #ProteinDesign @wehi-research.bsky.social
And thanks to Lyn Deng for creating such a cool ProteinDJ logo!
28.09.2025 22:16 — 👍 3 🔁 0 💬 0 📌 0Special 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)
28.09.2025 21:16 — 👍 3 🔁 0 💬 1 📌 0
Bindsweeper workflow
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)
28.09.2025 21:16 — 👍 2 🔁 0 💬 2 📌 0
Design modes for ProteinDJ
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)
28.09.2025 21:16 — 👍 3 🔁 0 💬 1 📌 0
ProteinDJ workflow
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)
28.09.2025 21:16 — 👍 2 🔁 0 💬 1 📌 0
ProteinDJ logo
I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5)
doi.org/10.1101/2025.09.24.678028 #proteindesign
And congratulations to Dylan for winning a poster prize!
13.02.2025 07:43 — 👍 4 🔁 1 💬 0 📌 0
Proud of our students from the Lucet Lab at WEHI who presented their posters at Lorne Proteins 2025. Well done to Dylan Silke, Emily Park, Jean-Max, and Lyn Deng! @jean-maxmazeri.bsky.social @wehi-research.bsky.social #LorneProteins2025 #LucetLab #WEHI
12.02.2025 03:41 — 👍 16 🔁 3 💬 2 📌 1
