
Co-Founder @ Xaira Therapeutics Former Baker Lab PostDoc at @UWproteindesign. Interested in generative modelling for molecular design. Views my own.
Joined September 2020
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We’ve been quiet about protein design at @Xaira_Thera . Here’s what we’ve been building:
Introducing X-Design, with results from two active drug programs that show what we think this field needs to deliver: speed to a useful lead, and access to targets that have resisted discovery.
→ 7 weeks from DNA synthesis to a preclinical lead on an oncology target, with the epitope and reagents already prepared.
→ A functional antibody antagonist against a challenging GPCR where conventional library screening AND llama immunization had failed.
The bar we set for our model goes well beyond binding.
The antibodies need to be human-like, functional, cross-reactive across species, and developable. Properties that have to come together in the same molecule for a program to move forward.
That’s what makes these results exciting to me: designs tested in the lab, meeting the requirements of real programs in our pipeline.
My bet is that the biggest impact of AI protein design will be expanding which diseases and targets we can pursue.
We want to choose targets because the biology is compelling and to build the ability to make the right molecules.
This is our first look at X-Design. Much more to come.
See our blog: xaira.com/news/de-novo-desig…
Joseph Watson retweeted
I am pleased to share that I have accepted a position @Stanford to start as an assistant professor in the department of statistics, with an affiliation in @StanfordData, this fall!
Joseph Watson retweeted
Replying to @CalSleeper
@CalSleeper really love travelling on your sleeper trains! Why not allow for booking 1 berth in cabins whilst keeping the option to book the full cabin? Would increase the number of people who could travel by train instead of flying! Feels quite a waste of berths atm 🤷♂️
Joseph Watson retweeted
Our review on diffusion models for protein structures and docking is out @HannesStaerk @GabriCorso Bowen Jing @BarzilayRegina Tommi Jaakkola. This summarize the advancements up to 2023. There have been lots of exciting new works since!
wires.onlinelibrary.wiley.co…
Joseph Watson retweeted
Impressive work from @UWproteindesign, @naterbennett0 @_JosephWatson @RobertRagotte @andrewjborst, @dejsee, @proleu & team: “Atomically accurate de novo design of single-domain antibodies”
Thanks for choosing Twist DNA to support this work 🧬
bit.ly/4a9mwyk
Joseph Watson retweeted
We’re excited to share our preprint where we show, for the first time, the atomically accurate design of VHH antibodies!
Joseph Watson retweeted
What's better than Diffusion for protein backbone generation?
(Stochastic) OT Flow Matching over SE(3)! link: arxiv.org/abs/2310.02391
New paper w/ @tara_aksa @FatrasKilian @Guillaume_hu @jarridrb @ChengHaoLiu1, @andreic_nica @MaksymKorablyov @mmbronstein @AlexanderTong7
1/5🧵
Joseph Watson retweeted
The Google Colab version of RFdiffusion with the conditional fold generation option worked well! We successfully placed two helices in the beta barrel structure. The RMSD between prediction and X-ray is only 0.3 Å!
colab.research.google.com/gi…
colab.research.google.com/gi…
Joseph Watson retweeted
Come check out our poster today at 4pm! We find that with a sequential Monte Carlo technique known as twisting we can use conditional sampling heuristics, like reconstruction guidance, to get exact inferences with additional compute.
Twisted Diffusion Sampling - Practical and Asymptotically Exact Conditional Sampling for Diffusion Models
Theoretically grounded conditional sampling for diffusion models with applications to inpainting, Bayesian inverse problems, protein design, ...
arxiv.org/abs/2306.17775
Joseph Watson retweeted
Now out in slightly shorter form :) nature.com/articles/s41586-0… @KotaroTsuboyama @JustasDauparas @LaineElodie @sokrypton
Joseph Watson retweeted
For scientists, #AlphaFold has helped accelerate the pace of potentially life-saving research. 🧬
Proteins with structures that look promising for certain uses, like binding to a cancer cell, can be identified more quickly than ever before.
Here's how: dpmd.ai/3q6ORDr
Joseph Watson retweeted
We are thrilled to share that Dr. Lynda Stuart has joined as our new Executive Director. With her extensive experience and dedication to healthcare as a human right, the future of protein design looks brighter than ever.
Learn more: ipd.uw.edu/2023/05/lynda-stu…
Joseph Watson retweeted
In case you missed it, make sure to check out our recent video where we dip our toes into the awesome world of AI protein generation!
youtu.be/4aG5g_52lFQ
Sending many thanks to @UWproteindesign, @_JosephWatson 's team and all else involved for open-sourcing #RFDiffusion :)
Joseph Watson retweeted
Tried RFdiffusion from @UWproteindesign in Colabfold by @sokrypton. Democratization of protein-design!! So amazing!! Exciting times ahead!! 🎉🙌
Joseph Watson retweeted
Been waiting for this--we have a stack of cancer-specific surface targets that need binders
Today we're making RF Diffusion, our guided diffusion model for protein design with potential applications in medicine, vaccines & advanced materials, free to use. The software has proven much faster and more capable than prior protein design tools.
bakerlab.org/2023/03/30/rf-d…
Joseph Watson retweeted
youtu.be/-H27Kv5duYA
🤯 Recent talk from David Baker @UWproteindesign , for those that missed it.
Joseph Watson retweeted
The recording of the RFDiffusion talk with @_JosephWatson @DaveJuergens is now available!
youtu.be/wIHwHDt2NoI
Joseph Watson retweeted
Excited to share our paper on peptide-MHC binding affinity prediction is now out in PNAS. This work was done by an amazing team of scientists from @UWproteindesign and @fredhutch
pnas.org/doi/10.1073/pnas.22…
Original thread: xitter.cf/AMotmaen/status/154743…
1/6 Can #AlphaFold learn from + & - labeled data to predict peptide binding better? w/ Phil Bradley @JustasDauparas @minkbaek @Mohamad_Abedi David Baker we present joint structure prediction-classification fine-tuning of #AF2 to classify pMHC binding.@UWproteindesign @fredhutch
Joseph Watson retweeted
While it's still 2022 I want to share some of the cool results in our @biorxivpreprint that we put up recently. (Work with @SusanaVazTor, Isaac Lutz, @PreethamVi, @_JosephWatson, @JosephRog
ers100 and many other incredibly talented individuals) biorxiv.org/content/10.1101/… (1/11)
Joseph Watson retweeted
Alpha-helical peptides captured by designed proteins. Biomedical applications abound. Special thanks from us to @_JosephWatson --- new binders from peptide sequence alone. Congrats to the big team @SusanaVazTor @proleu @fabian_hink @DaveJuergens
biorxiv.org/content/10.1101/…
























