Our latest AI tools for protein modeling & design were highlighted on the cover of
@ScienceMagazine
.
Read the open-access paper:
Use these tools for free:
RoseTTAFold All-Atom:
RFdiffusion All-Atom:
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.
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.
(1/8) Today we share the structures of protein complexes from nearly every core process in eukaryotic biology — from DNA repair to membrane trafficking.
This work builds on breakthroughs in coevolution & deep learning (
#Alphafold
,
#RoseTTAFold
).
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 ➡️
Learn more on YouTube ➡️
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
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."
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.
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
“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.
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.
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
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
.
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:
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.
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.
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.
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."
#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:
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.
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 ➡️
Short summary ⬇️
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:
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
"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."
.
@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:
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.
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 ➡️
Try it here ➡️
S. Korea has just approved a Phase 3 trial of the COVID nanoparticle vaccine we reported last year in Cell: All Phase 1/2 trial participants induced neutralizing antibodies.
@KingLabIPD
@veeslerlab
@UWMedicine
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 |
@PNASNews
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:
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.
"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."
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.
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: |
#ProteinDesign
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 🎉
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
#ProteinDesign
Researchers can access RF Diffusion through the open-source online platform ColabFold, which is part of the cloud-based Google Colaboratory.
The code is also available:
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.
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! 🔬
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.
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:
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.
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:
Commentary:
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 |
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:
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.
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
@_biojmg
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.
Protein designers can't make molecules that move, right?
Out today: "De novo design of tunable, pH-driven conformational changes"
@sciencemagazine
#proteindesign
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.
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:
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
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
Regulators in the UK have granted full approval to SKYCovione, the computationally designed COVID-19 vaccine pioneered by
@KingLabIPD
and
@veeslerlab
|
@UWMedicine
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
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."
#ProteinDesign
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:
New: Designed biosensors that can detect neutralizing antibodies against SARS-CoV-2 in blood.
These quantitative devices may aid in monitoring vaccine durability.
#proteindesign
with
@msdiamondlab
@veeslerlab
Thrilled to have hosted the Korean Minister of Health & Welfare at our institute last week. Minister Cho met with some of the minds behind SKYCovione, our pioneering COVID-19 vaccine developed with SK bioscience. Proud to showcase our groundbreaking work in protein design.
The University of Washington’s Institute for Protein Design has become a hub to galvanize de novo protein engineering, citizen science and much more since its founding in 2012 |
@NatureBiotech
Are you (or someone you know) interested in postdoctoral research in protein design? We are always accepting new
#postdocs
!
Join us for an informational open house — Jan 13, noon PT
Sign up here for Zoom link: |
#ProteinDesign
#postdocjobs
Our director David Baker recently shared his thoughts on the impact of AI on life sciences and healthcare startups. He spoke with Jenny Cronin at a
@UWCoMotion
event.
Congratulations to Frances Arnold on her
#NobelPrize
in
#chemistry
! She is true pioneer in showing the world the awesome power of proteins.👩🔬 📷:
@Caltech