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/...

Training bias and sequence alignments shape protein–peptide docking by AlphaFold and related methods

Protein-peptide interactions mediate many biological processes. Accurate structural models of protein-peptide complexes, determined by experiment or computational prediction, are essential for unders...

onlinelibrary.wiley.com

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

What research might be lost after the NIH’s cuts? Nature trained a bot to find out

We used machine-learning tools in an attempt to recreate the method for cutting funding, and then applied it to past US National Institutes of Health grants to reveal the broad-reaching consequences of such action.

go.nature.com

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...

Game Bub

An open-source FPGA retro-emulation handheld

crowdsupply.com

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🧵

Scaling down protein language modeling with MSA Pairformer

Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...

biorxiv.org

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!

Game Bub

An open-source FPGA retro-emulation handheld

crowdsupply.com

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...

Game Bub: open-source FPGA retro emulation handheld

I’m excited to announce the project I’ve been working on for the last year and a half: Game Bub, an open-source FPGA based retro emulation handheld, with support for Game Boy, Game Boy Color, and Game...

eli.lipsitz.net

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/...

NIH cuts billions of dollars in biomedical funding, effective immediately

The move halts a large slice of money for most universities and research institutions virtually overnight, imperiling vital research in everything from cancer to heart disease.

washingtonpost.com

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.

Dr. Rebecca Calisi-Rodríguez@rebeccacalisi.bsky.social · 2y ago

This will be the biggest game of Taboo the U.S. has ever seen.

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

Scientists as political advocates

Science, both teaching and doing, is under attack. The recent US presidential election of a person and platform with anti-science bias exemplifies this. The study of climate processes and patterns and...

science.org

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...

Jointly Embedding Protein Structures and Sequences through Residue Level Alignment

Residue Level Alignment integrates protein sequence and structure information in a self-supervised model, improving speed and precision in predicting protein binding and structural stability.

journals.aps.org