Here’s a preprint from the Keating Lab: www.biorxiv.org/content/10.6.... Foster Birnbaum and Amy E. Keating demonstrate that sequence design models, such as ProteinMPNN, are limited because they were trained only on native sequences.

now out in Protein Science! onlinelibrary.wiley.com/doi/10.1002/...

We used machine-learning tools in an attempt to recreate the method for cutting funding, and then applied it to past US NIH grants to reveal the broad-reaching consequences go.nature.com/4pBArFH

The Game Bub Crowd Supply campaign is live! And it's been redesigned with a new horizontal design. You can now back the campaign to get your very own pre-assembled Game Bub! www.crowdsupply.com/second-bedro...

Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

preprint is out for the first project of my phd! we investigated how structure prediction models work for protein-peptide complexes, where the peptide often doesn’t have a deep MSA / there’s no good paired MSA 🧵 (1/5) www.biorxiv.org/content/10.1...

How AlphaFold and related models predict protein-peptide complex structures https://www.biorxiv.org/content/10.1101/2025.06.18.660495v1

The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.

There’s been a lot of interest in Game Bub, so I’m going to be launching a crowdfunding campaign through @crowdsupply.bsky.social! Sign up for updates and to hear when the campaign goes live: www.crowdsupply.com/second-bedro... This will be an assembled product, not just a kit!

Published in the Chicago Sun Times today

I’m excited to announce Game Bub, an open-source FPGA emulation handheld with support for Game Boy and Game Boy Advance cartridges: eli.lipsitz.net/posts/introd...

Another assault on US competitiveness at a time when biomedicine is roaring with innovation, an own-goal in a high-stakes international tournament. Of course the real losers are American people needing medicines and cures. www.washingtonpost.com/health/2025/...

So one approach is to omit these words from your research. The other is for all of us to double down on including these words in EVERYTHING.

If you can, do something, speak up and act up. www.science.org/doi/10.1126/...

A weekend project from a while back -- this little package (with no dependencies) allows you to interact with pymol remotely. I use it a lot for my protein design workflows together with @biotite.bsky.social. Just `pip install pymol-remote`

✨new work from our lab!✨ RLA is a contrastive-learning approach that assesses sequence-structure compatibility by aligning sequence and structure machine learning representations! RLA can successfully filter protein binder designs. 1/3 🧶 journals.aps.org/prxlife/abst...