@naterbennett0

Co-Founder at Xaira Therapeutics. De novo protein binder design. Former Postdoctoral Scholar at @UWproteindesign.

 Seattle, WA
Joined June 2022
  • Tweets60
  • Following194
  • Followers1.1K
8Media
We’re excited to share our preprint where we show, for the first time, the atomically accurate design of VHH antibodies!
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Nate Bennett retweeted
Phil Leung
@proleu15 Aug 2024
Love this article by @schubertcm @geekwire on what we're trying to do here in #Seattle at @Xaira_Thera @JustasDauparas @naterbennett0 geekwire.com/2024/inside-the…
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Want a quick primer on the science behind why Xaira just launched with a $1B+ seed round? The wonders of peer view and publishing have very conveniently decided to just publish our review on how generative AI is transforming de novo protein design! sciencedirect.com/science/ar…
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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
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We’re really happy to share our preprint demonstrating the atomically-accurate design of single-domain antibodies (VHHs) with RFdiffusion!
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We had so many amazing collaborators on this project: @dejsee, @wanderingriti, @proleu, @SingerBenedikt, @SusanaVazTor, as well as many Twitter-less collaborators!
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This work is a proof-of-concept and needs to be refined before it is on-par with RFdiffusion for mini binder design. I'm incredibly excited, however, about the potential of this type of technology for therapeutic design and I can't wait to see where this leads!
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Replying to @proleu
@proleu and I are excited to see our work on multistate design of hinge proteins finally published as a peer-reviewed paper science.org/doi/full/10.1126…

Design of stimulus-responsive two-state hinge proteins

A two-state design of protein switches that couple effector binding to a conformational change is discussed.

science.org
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nature
@Nature11 Jul 2023
Digital art techniques can now devise custom, working biomolecules on demand. These proteins could form the basis for vaccines, therapeutics and biomaterials. Read the full story: nature.com/articles/d41586-0…
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It's so great to see our RFdiffusion paper now live @Nature. This article from @ewencallaway gives a great overview of RFdiffusion and protein diffusion models more broadly, and also highlights some of the ways people are already using it in their own research!
nature
@Nature11 Jul 2023
Digital art techniques can now devise custom, working biomolecules on demand. These proteins could form the basis for vaccines, therapeutics and biomaterials. Read the full story: nature.com/articles/d41586-0…
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Nate Bennett retweeted
Tim Huddy@tim_huddy12 Jun 2023
Geometrically standardized features give @LEGO_Group blocks their ability to be intuitively assembled into structures. Here we show that designed proteins can be made to a similar standard, enabling useful features in nanomaterials such as scalable size: biorxiv.org/content/10.1101/…

Blueprinting expandable nanomaterials with standardized protein building blocks

A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The...

biorxiv.org
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Nate Bennett retweeted
Minkyung Baek
@minkbaek26 May 2023
Introducing RoseTTAFold2: Protein structure prediction AI that combines the best of AlphaFold2 and RoseTTAFold. Even without IPA and triangle attention, RF2 achieves comparable performance to AlphaFold2. biorxiv.org/content/10.1101/…

Efficient and accurate prediction of protein structure using RoseTTAFold2

AlphaFold2 and RoseTTAFold predict protein structures with very high accuracy despite substantial architecture differences. We sought to develop an improved method combining features of both. The...

biorxiv.org
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.@naterbennett0 and colleagues show how deep learning can be used to improve the hit-rate of de novo protein binder design 10-fold. @UWproteindesign #DeepLearning #proteindesign #BiotechNatureComms nature.com/articles/s41467-0…
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The Baker Lab has a new #openaccess paper in @NatureComms showing that dramatic improvements can be achieved when deep learning software is used to design protein-binding proteins. Full paper ➡️ nature.com/articles/s41467-0… Short summary ⬇️ bakerlab.org/2023/05/08/deep…
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It’s exciting to see our work on improving binder design with deep learning methods published in Nature Communications! nature.com/articles/s41467-0…
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more replies
This method is what we use for sequence design and in silico filtering of RFdiffusion protein binder backbones! RFdiffusion is already open source and we are making this method free and open source as well: github.com/nrbennet/dl_binde…

GitHub - nrbennet/dl_binder_design

Contribute to nrbennet/dl_binder_design development by creating an account on GitHub.

github.com
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Protein binder design has never been easier and we are excited to see what you design! A big thanks to my co-lead on this paper: Brian Coventry (who is not on Twitter).
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