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Zachary Wu

@zacharywu.bsky.social
1.7K followers 184 following 8 posts

Researcher at Google DeepMind. Previously Arnold group at Caltech. Making useful molecules!

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Reposted by Zachary Wu
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 20h
Combine a chemical knowledge, generative modeling, and structure prediction into a pipeline that can design enzymes for new-to-nature chemistry. @zacharywu.bsky.social @alexechu.bsky.social @francesarnold.bsky.social @pushmeet.bsky.social @juewang.bsky.social www.biorxiv.org/content/10.6...
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Reposted by Zachary Wu
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 19/06/2025
Physics-based design of efficient Kemp eliminases @lynnkamerlin.bsky.social www.nature.com/articles/s41...
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Reposted by Zachary Wu
Frances Arnold @francesarnold.bsky.social · 20/01/2025
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
tinyurl.com
PCAST Reports (2020-2025)
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Reposted by Zachary Wu
Keith Robison @omicsomics.bsky.social · 08/01/2025
www.nature.com/articles/s41...
nature.com
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...
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Reposted by Zachary Wu
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 18/12/2024
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
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.
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Reposted by Zachary Wu
Noelia Ferruz @noeliaferruz.bsky.social · 18/12/2024
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
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Reposted by Zachary Wu
Sander Dieleman @sedielem.bsky.social · 16/12/2024
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...
blog.google
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.
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Reposted by Zachary Wu
Marwin Segler @marwinsegler.bsky.social · 09/12/2024
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
arxiv.org
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...
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Reposted by Zachary Wu
Amy Lu @amyxlu.bsky.social · 06/12/2024
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 🧵
overview of results for PLAID!
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Zachary Wu @zacharywu.bsky.social · 08/12/2024
Lots coming for protein design!
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Reposted by Zachary Wu
Frank Noe @franknoe.bsky.social · 06/12/2024
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.
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Reposted by Zachary Wu
Ben Lehner @benlehner.bsky.social · 03/12/2024
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...
biorxiv.org
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...
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Reposted by Zachary Wu
Sander Dieleman @sedielem.bsky.social · 15/11/2024
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!
drscotthawley.github.io
blog - Flow With What You Know
Basic physics provides a “straight, fast” way to get up to speed with flow-based generative models
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Zachary Wu @zacharywu.bsky.social · 25/11/2024
We also have an opening in Materials! Reminder: our London Wetlab position application closes Wednesday
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Reposted by Zachary Wu
Eric Topol @erictopol.bsky.social · 22/11/2024
Discovery of a biodegradable, fully recyclable plastic www.science.org/doi/10.1126/...
science.org
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...
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Reposted by Zachary Wu
Diego del Alamo @delalamo.xyz · 20/11/2024
RFdiffusion for macrocycles www.biorxiv.org/content/10.1...
Figure 1: RFpeptides is a diffusion-based pipeline for the de novo design of protein-binding macrocycles.
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Zachary Wu @zacharywu.bsky.social · 18/11/2024
Come join our London wet-lab team! Deadline to apply is next Wednesday boards.greenhouse.io/deepmind/job...
boards.greenhouse.io
Laboratory Research Scientist, Protein Design, Science
London, UK
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