Zachary Wu

Physics-based design of efficient Kemp eliminases

@lynnkamerlin.bsky.social

www.nature.com/articles/s41...

19.06.2025 21:18 — 👍 22    🔁 8    💬 0    📌 0

PCAST Reports (2020-2025)

The White House website has been wiped clean, but thanks to @erichorvitz.bsky.social , all the Biden #PCAST reports are available below. I want to thank the #PCAST members, all of whom donated their time and expertise to helping policy be science-based. tinyurl.com/2acnv2nh

20.01.2025 22:53 — 👍 95    🔁 25    💬 3    📌 5

Site-saturation mutagenesis of 500 human protein domains - Nature Large-scale experimental analysis of Human Domainome 1, a library containing more than 500,000 missense mutation variants across more than 500 human protein domains, reveals that 60% of pathogenic mis...

www.nature.com/articles/s41...

08.01.2025 18:05 — 👍 47    🔁 14    💬 0    📌 1

Fun read, even though I was too engrossed and ended up getting lost in the office

19.12.2024 18:07 — 👍 0    🔁 0    💬 0    📌 0

In-context genomic modeling and design with Evo.

120 billion base pairs of AI-generated genomic sequences with SynGenome.

Evo generates functional anti-CRISPR proteins with no homology to known proteins.

Evo generates functional toxin-antitoxin protein-protein interactions with remote homology to nature.

A protein's position in the genome in relation to other genes is informative about function, so a genomic language model can be prompted to generate
- toxin/antitoxin pairs
- anti-CRISPR proteins

+ a database of 120B synthetic base pairs

www.biorxiv.org/content/10.1...

@brianhie.bsky.social

18.12.2024 22:14 — 👍 60    🔁 19    💬 1    📌 0

Protein language models excel at generating functional yet remarkably diverse artificial sequences.

They however fail to naturally sample rare datapoints, like very high activities.

In our new preprint, we show that RL can solve this without the need for additional data:

arxiv.org/abs/2412.12979

18.12.2024 21:06 — 👍 58    🔁 15    💬 1    📌 1

State-of-the-art video and image generation with Veo 2 and Imagen 3 We’re rolling out a new, state-of-the-art video model, Veo 2, and updates to Imagen 3. Plus, check out our new experiment, Whisk.

Here's Veo 2, the latest version of our video generation model, as well as a substantial upgrade for Imagen 3 🧑‍🍳🚢

(Did I mention we are hiring on the Generative Media team, btw 👀)

blog.google/technology/g...

16.12.2024 17:35 — 👍 60    🔁 17    💬 0    📌 1

I recently made a new twitter account to reserve a username. The baseline feed is quite scary and a good push 😬

13.12.2024 23:17 — 👍 3    🔁 0    💬 0    📌 0

*and congrats!!

13.12.2024 19:07 — 👍 1    🔁 0    💬 0    📌 0

Looks like the focus is on small molecule chemical hazards? Or will macromolecule hazards also be of interest?

13.12.2024 19:06 — 👍 0    🔁 0    💬 2    📌 0

Famous? The description made it seem like one of many 😂

13.12.2024 19:03 — 👍 0    🔁 0    💬 0    📌 0

Chimera: Accurate retrosynthesis prediction by ensembling models with diverse inductive biases Planning and conducting chemical syntheses remains a major bottleneck in the discovery of functional small molecules, and prevents fully leveraging generative AI for molecular inverse design. While ea...

new preprint on chemical synthesis ML models

- showing how to combine multiple models in a principled way
- modern Transformers + GNN to featurize chemical reaction:
- new insights in where the models shine
+ bonus: find the quirky named reaction!

Feedback welcome!

arxiv.org/abs/2412.05269

09.12.2024 02:19 — 👍 83    🔁 27    💬 4    📌 1

overview of results for PLAID!

1/🧬 Excited to share PLAID, our new approach for co-generating sequence and all-atom protein structures by sampling from the latent space of ESMFold. This requires only sequences during training, which unlocks more data and annotations:

bit.ly/plaid-proteins
🧵

06.12.2024 17:44 — 👍 121    🔁 37    💬 1    📌 3

Lots coming for protein design!

08.12.2024 10:33 — 👍 4    🔁 1    💬 0    📌 0

Introducing Biomolecular Emulator (BioEmu). We build on AlphaFold evoformer representation of protein sequence, then sample 3D structures from equilibrium ensemble with diffusion model. From this sample, we can compute states, probabilities and understand mechanisms.

06.12.2024 08:38 — 👍 29    🔁 4    💬 1    📌 0

A pharmacological chaperone stabilizer rescues the expression of the vast majority of pathogenic variants in a G protein-coupled receptor Reduced protein stability is the most frequent mechanism by which rare missense variants cause disease. A promising therapeutic avenue for treating destabilizing variants is pharmacological chaperones...

Can a single small molecule rescue the stability of nearly all mutations in a protein?
Our new preprint by Taylor Mighell
www.biorxiv.org/content/10.1...
thread on the other place: x.com/taylor_mighe...

03.12.2024 09:40 — 👍 68    🔁 24    💬 3    📌 1

blog - Flow With What You Know Basic physics provides a “straight, fast” way to get up to speed with flow-based generative models

This blog post by @drscotthawley.bsky.social provides a very accessible overview of flow matching / rectified flow and reflow, based on intuitions from physics, rather than starting from probability distributions. The visualisations and animations are excellent, and the whole thing is also a colab!

15.11.2024 20:31 — 👍 79    🔁 15    💬 1    📌 1

We also have an opening in Materials! Reminder: our London Wetlab position application closes Wednesday

25.11.2024 17:25 — 👍 5    🔁 0    💬 0    📌 0

Mechanically strong yet metabolizable supramolecular plastics by desalting upon phase separation Plastics that can metabolize in oceans are highly sought for a sustainable future. In this work, we report the noncovalent synthesis of unprecedented plastics that are mechanically strong yet metaboli...

Discovery of a biodegradable, fully recyclable plastic
www.science.org/doi/10.1126/...

22.11.2024 15:23 — 👍 254    🔁 62    💬 1    📌 6

Figure 1: RFpeptides is a diffusion-based pipeline for the de novo design of protein-binding macrocycles.

RFdiffusion for macrocycles www.biorxiv.org/content/10.1...

20.11.2024 18:48 — 👍 60    🔁 8    💬 1    📌 0

Laboratory Research Scientist, Protein Design, Science London, UK

Come join our London wet-lab team! Deadline to apply is next Wednesday boards.greenhouse.io/deepmind/job...

18.11.2024 15:47 — 👍 1    🔁 1    💬 0    📌 0