We create proteins that solve challenges in medicine, technology & sustainability 🟡 2024 Nobel in Chemistry 📍@UWMedicine — ipd.uw.edu/join-us/
Seattle, WA
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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…
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01. Today we report the computational design of highly efficient enzymes. Lab testing confirms that these novel luciferases can recognize specific synthetic substrates and efficiently catalyze the emission of light.
nature.com/articles/s41586-0…
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(1/8) Today we share the structures of protein complexes from nearly every core process in eukaryotic biology — from DNA repair to membrane trafficking.
science.org/doi/10.1126/scie…
This work builds on breakthroughs in coevolution & deep learning (#Alphafold, #RoseTTAFold).
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Generative AI for protein design is now one click away. We've launched a new platform that puts powerful tools behind a simple web interface, making #proteindesign accessible to anyone.
Try it here ➡️ huggingface.co/spaces/merle/…
Learn more on YouTube ➡️ piped.video/bS71K2U0amA
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Design of protein binding proteins from target structure alone | @Nature
Our approach now enables targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications. #proteindesign
nature.com/articles/s41586-0…
ALT Small proteins designed from scratch to bind the insulin receptor and a component of the influenza virus, among other targets.
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Nobel Laureate David Baker on the phone with fellow awardees Demis Hassabis and John Jumper. The trio discussed how their teams have inspired one another and what the future may hold.
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Congrats to David Baker who, together with Demis Hassabis & John Jumper, just received the Frontier of Knowledge Award in Biology & Biomedicine.
"[Our progress is] the result of many hundreds of brilliant minds all working together. This award is as much theirs as it is mine."
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Today we report the design of proteins that bind to disordered targets. This design strategy focuses on features common to the peptide backbone and can be used to generate binders for disordered proteins.
nature.com/articles/s41586-0…
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Scientists in the Baker Lab have designed new proteins that change shape upon binding a target molecule. This research opens the door to new applications in drug delivery, environmental sensing & more.
@FloPraetorius, @definitelyphil
bakerlab.org/2023/08/17/swit…
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“This really is a big deal” — David Baker on today's #AlphaFold news.
From our team to @DeepMind: Congratulations! You have electrified this important field. We look forward to what can be accomplished in the coming years.
technologyreview.com/2020/11…
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Congratulations to our director, David Baker, on winning a Breakthrough Prize in Life Sciences!
forbes.com/sites/alexknapp/2…
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Today we report the use of reinforcement learning, a strategy used to solve games like chess and Go, to a challenge in protein design. This milestone in using #AI for science may enable more effective cancer treatments & new biodegradable textiles.
science.org/doi/10.1126/scie…
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As researchers, innovators, and communities worldwide celebrate this remarkable achievement, we look forward to the groundbreaking discoveries and life-changing solutions that still lie ahead—solutions made possible by the visionary work that has earned David Baker a Nobel Prize.
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Rosetta Commons is pleased to once again offer (paid) undergraduate internships and postbac fellowships in biomolecular structure prediction and design!
Learn about #deeplearning breakthroughs and how to apply them to create new therapies, vaccines & biotechnologies. 1/3
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We are honored to see our work on protein structure prediction recognized as the 2021 Breakthrough of the Year.
We also applaud @DeepMind for invigorating the field and contributing so much to open science.
All areas of computational and molecular biology will be transformed.
AI algorithms can now churn out predictions for the 3D shapes of proteins with a precision matching that of painstaking laboratory techniques. The programs, and the blizzard of protein structures they have revealed, are Science’s 2021 #BOTY. fcld.ly/twr28jc
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SKYCovione, a COVID-19 vaccine developed by @KingLabIPD & @veeslerlab, has just won full approval abroad!🇰🇷This protein-based vaccine outperforms Oxford/AstraZeneca's and does not require freezing. It is our first designed protein medicine.
Learn more: ipd.uw.edu/2022/06/covid-19-…
ALT The vaccine, now called SKYCovione, is a tiny ball of protein studded with 60 copies of the SARS-CoV-2 receptor-binding domain.
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Just as convincing images of cats can be generated using artificial intelligence, new proteins can now be made using similar tools. In a new report in @Nature, we describe a neural network approach for “hallucinating” proteins with new, stable structures.
nature.com/articles/s41586-0…
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David Baker will present the @MRC_LMB 2021 Max Perutz Lecture, titled ‘The coming of age of de novo protein design’ at 8:00am (Pacific) on Tuesday, April 27. Attendance via Zoom is free & open to all.
mrc-lmb.cam.ac.uk/2021-max-p…
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Today we report the design of new proteins that cluster antibodies into dense nanoparticles. In lab testing, such clustered Abs neutralize SARS-CoV-2 pseudovirus, enhance cell signaling, and promote T cell growth more effectively than free antibodies.
science.sciencemag.org/conte…
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Our latest AI tools for protein modeling & design were highlighted on the cover of @ScienceMagazine.
Read the open-access paper: science.org/doi/10.1126/scie…
Use these tools for free:
RoseTTAFold All-Atom: github.com/baker-laboratory/…
RFdiffusion All-Atom: github.com/baker-laboratory/…
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This is a historic day for protein design: New computer-generated proteins fight #cancer with fewer side effects.
nature.com/articles/s41586-0… #immunotherapy #proteindesign #neoleukin @nature
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David Baker, together with Demis Hassabis & John Jumper of @DeepMind, has received the Frontiers of Knowledge Award from @FundacionBBVA for "contributions to the use of A.I. for the accurate prediction of the 3D structure of proteins."
ipd.uw.edu/2023/01/frontiers…
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Robust de novo design of protein binding proteins from target structural information alone
biorxiv.org/content/10.1101/…
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#RoseTTAFold: Accurate prediction of protein structures and interactions using a three-track neural network. By @minkbaek et al, @ScienceMagazine
science.sciencemag.org/conte…
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#ProteinMPNN, which is now available free on the open-source software repository GitHub, will give researchers the tools to make unlimited new designs. “The challenge, of course, is what are you going to design?”
GitHub: github.com/dauparas/ProteinM…
technologyreview.com/2022/09…
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Today we report the design of protein assemblies made from modular parts. These complexes — which adopt linear, branching, or closed-loop architectures — contain up to 6 unique proteins, each of which remains soluble in the absence of binding partners.
science.org/doi/10.1126/scie…
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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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Accurate de novo design of membrane-traversing macrocycles | @CellCellPress
cell.com/cell/fulltext/S0092…
ALT We use computational design coupled with experimental characterization to systematically investigate the design principles for macrocycle membrane permeability and oral bioavailability.
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The first episode of @BakerLabPodcast is live. Meet Mohamad Abedi, who went from being a Palestinian refugee to a postdoctoral researcher. His journey proves that science can be a creative and transformative process.
Apple: podcasts.apple.com/us/podcas…
Spotify: open.spotify.com/show/32pWWp…
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Ready to learn about protein design? Our beginner's guide breaks down this complex field into easy-to-understand concepts. Discover the potential of proteins to transform our world: ipd.uw.edu/2023/05/what-is-p…
ALT An artist’s depiction of a protein structure emerging from a computer chip.
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🔴 LIVE in 25 minutes: Computational Protein Design Then & Now (1988-2024)
A free one-hour webinar featuring:
David Baker (UW)
Steve Mayo (Caltech)
Bill DeGrado (UCSF)
Brian Kuhlman (UNC)
piped.video/live/BuJGTn7OhxQ
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David Baker will soon present at the NIH Director's Wednesday Afternoon Lecture Series. His talk is titled The Coming of Age of De Novo Protein Design
Wednesday, Dec 14, 2:00pm ET
Watch live at videocast.nih.gov
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"De novo protein design has reached an inflection point, researchers say. AI-powered protein design is becoming very real and very usable, thanks to technological advances in the development of algorithms and the hardware that runs them."
cen.acs.org/physical-chemist…
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.@ScienceMagazine has published a beautiful profile of our efforts to design a vaccine that protects against many coronaviruses at once. A close collaboration between NIAID, @KingLabIPD , @veeslerlab, @WardLab1, & others.
The dream vaccine: science.sciencemag.org/conte…
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Did you know David Baker just launched a podcast? The first episode features trainee @Mohamad_Abedi. Born a Palestinian refugee, Mohamad never dreamed he’d grow up to become the scientist he is today.
Apple Podcasts: podcasts.apple.com/us/podcas…
Spotify: open.spotify.com/show/32pWWp…
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Today we report new #deeplearning approaches for functional #proteindesign. We use these to generate immunogens, receptor traps, metalloproteins, enzymes, and binder proteins. We validate the designs using in silico and lab tests.
science.org/doi/10.1126/scie…
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Generative AI for protein design is now one click away. We've launched a new platform that puts powerful tools behind a simple web interface, making #proteindesign accessible to everyone.
Full video ➡️ piped.video/bS71K2U0amA
Try it here ➡️ huggingface.co/spaces/merle/…
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Have you had a chance to use RFdiffusion?
We would love to hear about it! Please share your story here or send us an email: contact@ipd.uw.edu
bakerlab.org/2023/03/30/rf-d…
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Computational design of mechanically coupled axle-rotor protein assemblies science.org/doi/10.1126/scie…
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Watch Nobel Laureate David Baker explain his life's work in under 9 minutes.
→ What is protein design?
→ What will it lead to?
→ What's next for David?
@UW @UWMedicine @HHMINEWS @NobelPrize #proteindesign
piped.video/watch?v=g96tXNwr…
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S. Korea has just approved a Phase 3 trial of the COVID nanoparticle vaccine we reported last year in Cell: cell.com/cell/fulltext/S0092… All Phase 1/2 trial participants induced neutralizing antibodies. @KingLabIPD @veeslerlab @UWMedicine
reuters.com/world/asia-pacif…
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Proteins are life’s most important molecules. And in the words of the Nobel committee, Baker “has succeeded with the almost impossible feat of building entirely new kinds of proteins.”
ipd.uw.edu/2024/10/david-bak…
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A #deeplearning approach to protein design: When combined with detailed physical models, AI can capture properties normally only accessible through large-scale simulations.
Protein sequence design by conformational landscape optimization pnas.org/content/118/11/e201… | @PNASNews
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IPD director David Baker, together w John Jumper and @DemisHassabis of DeepMind, will receive the 2022 Wiley Prize in Biomedical Sciences for pioneering work on protein structure prediction. Their award lectures will be streamed April 1. Learn more at: newsroom.wiley.com/press-rel…
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Dr. Anthony Fauci shared some news with Congress about our collaborative influenza vaccine research. Phase 1 trials are now underway!
Paper is nature.com/articles/s41586-0… by @DanLikeProteins, @KingLabIPD, @kanekiyom, @BarneyGrahamMD, & many more.
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We're advancing a new global agreement signed by 100+ leading scientists to ensure AI technologies for protein design are developed responsibly. This field can deliver medicines, vaccines, and other innovations that benefit all.
ipd.uw.edu/2024/03/our-commi…
responsiblebiodesign.ai/
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"Baker and his colleagues tested their strategy on 12 target proteins. [T]he researchers wound up with miniproteins that bound as strongly as, if not stronger than, most antibodies do."
science.org/content/article/…
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We are mourning the loss of Dan Tawfik, a brilliant researcher and longtime friend of the institute. His scientific accomplishments will endure, as will his kindness, generosity, and humor. Dan made the world a better place.
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"For the first time, we can create new proteins from scratch that do exactly what we want them to do."
(Entrevista en español) elpais.com/ciencia/2023-02-1…
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New protein-based biosensors have been designed from scratch to enable direct detection of #SARSCoV2 particles. Additional sensors that detect COVID-19 antibodies are also described in our latest preprint: biorxiv.org/content/10.1101/… | #ProteinDesign
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“What we need are new proteins that can solve modern-day problems, like cancer and viral pandemics,” Dr. Baker said. “We can’t wait for evolution.”
nytimes.com/2023/01/09/scien…
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Our Institute was founded ten years ago with a small team and a big vision. Now both are larger than ever! Thank you to everyone who helped make this first decade so much fun. Here's to many more 🎉
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De novo design of picomolar SARS-CoV-2 miniprotein inhibitors biorxiv.org/content/10.1101/… | @biorxivpreprint
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In a new report, we describe the de novo design & characterization of selective ion channels, as well as larger pores that permit the passage of fluorescent molecules thru cell walls.
Computational design of transmembrane pores
| nature.com/articles/s41586-0… | @nature #ProteinDesign
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Researchers can access RF Diffusion through the open-source online platform ColabFold, which is part of the cloud-based Google Colaboratory. colab.research.google.com/gi…
The code is also available: github.com/RosettaCommons/RF…
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Our trRosetta #deeplearning method has been applied to all protein families of unknown structure, yielded 6,370 new protein models. All now available in @PfamDB, with 3D structure views and contact maps in @InterProDB. Happy exploring! 🔬
ipd.uw.edu/2021/03/trrosetta…
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New in @NatureComms: "Improved protein structure refinement guided by #deeplearning based accuracy estimation" nature.com/articles/s41467-0…
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The COVID19 vaccine developed by @KingLabIPD & @VeeslerLab has met its Phase 3 trial goals and is now under review for full authorization in Korea.
SK bioscience, the company leading clinical development abroad, found the vaccine outperformed Oxford/AstraZeneca’s in the clinic.
ALT The vaccine, now called SKYCovione, is a tiny ball of protein studded with 60 copies of the SARS-CoV-2 receptor-binding domain (shown in red). Image: Ian C Haydon / UW Medicine Institute for Protein Design
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Peptide-binding specificity prediction using fine-tuned protein structure prediction networks | PNAS
@AMotmaen, @UWBiochemistry pnas.org/doi/10.1073/pnas.22…
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Deep learning has revolutionized protein structure modeling. Here, David Baker and @minkbaek relate #AlphaFold and #RoseTTAFold to classical approaches to structure prediction and discuss the areas of structural biology that are likely to be transformed.
rdcu.be/cEMXx
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Tired: Writing your name on a grain of rice ✍️
Wired: Writing your name into an AI-generated protein 🧬
Try it for free in your browser ➡️ huggingface.co/spaces/merle/…
just generated a protein with my name in it, very cool stuff from @UWproteindesign
huggingface.co/spaces/merle/…
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RF Diffusion was developed by a team of computational biologists from @UWProteinDesign, @Columbia & @AIHealthMIT.
Our thanks to @sokrypton for implementing it onto the ColabFold platform.
colab.research.google.com/gi…
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Accurate prediction of protein structures and interactions using a 3-track network
biorxiv.org/content/10.1101/…
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From modeling viral proteins to creating candidate vaccines, our scientists are taking on COVID-19.
• 11,000+ de novo antiviral proteins are in testing
• Nanoparticle vaccines already in animals 🐁 ( @KingLabIPD, @veeslerlab, @NIH)
Learn more: ipd.uw.edu/2020/02/rosettas-…
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Today's an exciting day!
After many years of work, we're thrilled to report our latest advance in citizen science: nature.com/articles/s41586-0…
@Foldit @UWBiochemistry @uwcse @RutgersU @dartmouth @Northeastern @HHMINEWS #citizenscience #proteindesign @nature
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Deep networks trained to predict native protein structures from their sequences can be inverted to design new proteins | @biorxivpreprint
biorxiv.org/content/10.1101/…
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A COVID19 nanoparticle vaccine designed @UWMedicine (@KingLabIPD, @veeslerlab) has achieved its Phase 1/2 clinical goals! In a trial led by SK Bioscience, the vaccine was found safe and generated high levels of neutralizing antibodies. Ph3 is underway.
ipd.uw.edu/2021/11/covid-19-…
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Honored to see our work on #deeplearning for protein structure prediction featured on the cover of @ScienceMagazine. Research was led by the tremendously talented @minkbaek.
Article: science.sciencemag.org/conte…
Commentary: science.sciencemag.org/conte…
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New: Synthetic proteins designed to bind Spike on SARS-CoV-2 provide starting points for COVID-19 therapeutics. @UWMedicine @veeslerlab @WUSTLmed
De novo design of picomolar SARS-CoV-2 miniprotein inhibitors | science.sciencemag.org/conte…
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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…
ALT A bright photograph of Dr. Lynda Stuart smiling and looking into the camera.
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Today our admin team met with @RepJayapal to celebrate new Federal investments in 10 key projects across the Seattle area. Our request will enable the purchase of advanced laboratory equipment that will help us discover new cures for current and future pandemics.
ALT Congresswoman Pramila Jayapal speaks at a podium in Seattle.
ALT Congresswoman Pramila Jayapal hands an enlarged check for $550,000 to a team from the University of Washington Institute for Protein Design. The funding will support the purchase of advanced research equipment.
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De novo design of protein homodimers containing tunable symmetric protein pockets
pnas.org/doi/10.1073/pnas.21…
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Today we report the design of protein sequences that adopt more than one well-folded structure, reminiscent of viral fusion proteins. This research moves us closer to creating artificial protein systems with reliable moving parts. #ProteinDesign
pnas.org/content/early/2020/…
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Hej from Stockholm! 🇸🇪
David Baker has invited >30 current trainees, >100 scientific peers, and members of his family to join him as he receives the #NobelPrize in #Chemistry.
Want to join in? You may stream or later watch several Nobel Week events: nobelprize.org/ceremony/prog…
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Protein designers can't make molecules that move, right?
Out today: "De novo design of tunable, pH-driven conformational changes"
science.sciencemag.org/conte… @sciencemagazine #proteindesign
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We think it's the third option: three billion years of natural selection is not nearly enough time to sample even one percent of the vast protein universe. There have got to be remarkable —and useful — molecules still out there.
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There’s a new profile of our research out today in the @NewYorker. Features perspectives from @francesarnold & other luminaries in the field
#ProteinDesign #MachineLearning #SARSCoV2 @Foldit @RosettaAtHome | @SilverJacket newyorker.com/tech/annals-of…
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New this week: @definitelyphil and @FloPraetorius have created “hinge” proteins that adopt two shapes: one with ligand, one without.
This control over molecular motion sets the stage for new applications in smart medicines and beyond.
science.org/doi/10.1126/scie…
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Reminder: Researchers on our COVID-19 vaccine design team will soon be answering questions live for a Reddit AMA!
They'll be joined by @Foldit scientists working on antivirals.
Monday, Mar. 30
11:00 AM PT
2:00 PM ET
6:00 PM GMT
Look for us: teddit.net/r/Coronavirus
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Preclinical data out today: Our nanoparticle vaccine candidate for COVID-19 elicits ten times more neutralizing antibodies than vaccination with Spike alone.
Led by @KingLabIPD, @veeslerlab | #ProteinDesign
New Article now online: Elicitation of potent neutralizing antibody responses by designed protein nanoparticle vaccines for SARS-CoV-2 zpr.io/HFvZP
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Congrats to Brian Koepnick, Baker lab, for successfully defending his PhD today!
Brian has helped a community of over 700k citizen scientists gain access to advanced tools for protein design. @Foldit #citizenscience
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Dive inside our efforts to design second-generation COVID-19 vaccines & treatments with this new feature in Scientific American.
@coronalexington, @veeslerlab, @KingLabIPD, @UWMedicine, @BarneyGrahamMD | @sciam, @rowanjacobsen
scientificamerican.com/artic…
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De novo design of modular and tunable protein biosensors nature.com/articles/s41586-0… | @Nature
New sensors detect coronavirus proteins and antibodies ipd.uw.edu/2021/01/covid-ant… | @UWMedicine
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Regulators in the UK have granted full approval to SKYCovione, the computationally designed COVID-19 vaccine pioneered by @KingLabIPD and @veeslerlab | @UWMedicine
gov.uk/government/news/skyco…
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Congratulations to IPD founder David Baker for being named a 2018 Highly Cited Researcher. Dr Baker's publications are among the world's most influential, having achieved the highest percentile of peer citations in Biology & Biochemistry #HighlyCited2018 @webofscience
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Today in @Nature: Programmable design of orthogonal protein heterodimers nature.com/articles/s41586-0…
cc: @UWBiochemistry
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In this new video, the team at @SciShow explains how A.I. is transforming protein science.
"The future of biology is starting to take shape." — @hankgreen
WATCH: piped.video/watch?v=gVzPMZqO…
#RoseTTAFold #AlphaFold #AlphaFold2
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New reporting on our de novo designed COVID-19 antivirals: "When spritzed up the noses of mice & hamsters, it also appears to protect animals from becoming seriously sick." nytimes.com/2020/11/21/scien… #ProteinDesign
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Our friends at CellSpace are bringing beauty to this dark moment with a galley of art focused on the molecular biology of SARS-CoV-2. Included in the collection is this piece by @dr_opatel depicting our antiviral miniproteins (CC-BY-4.0)
Full gallery: ccsb.scripps.edu/new-ways-of…
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New from our spinout @neoleukin: "De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2" | @ScienceMagazine #ProteinDesign
science.sciencemag.org/conte…
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ICYMI: AI tools are designing entirely new proteins that could transform medicine nature.com/articles/d41586-0…
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