A diffusion model for protein design

A team led by Baker Lab scientists Joseph Watson, David Juergens, Nate Bennett, Brian Trippe, and Jason Yim has created a powerful new way to design proteins by combining structure prediction networks and generative diffusion models. The team demonstrated extremely high computational success and tested hundreds of A.I.-generated proteins in the lab, finding that many …

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Annual Report 2022

  Protein design reached two major milestones this year: Our Institute succeeded in producing its first fully-approved medicine, and our spinout companies have together raised over one billion dollars in capital.  We are pleased to present this overview of the progress made at the Institute for Protein Design during the past year. 2022 Annual Report

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Biosensor startup Monod secures $25M seed financing

Monod Bio, a life sciences company developing custom diagnostic biosensors that emit light to detect specific biomolecules of interest, today announced it has raised a $25M seed financing round. The round was led by Matrix Capital, with participation from the Global Health Investment Corporation, Cercano Management, The Washington Research Foundation, Boom Capital Ventures, Sahsen Ventures, …

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Celebrating our 10-year Anniversary

  This week we celebrated the 10-year anniversary of the Institute for Protein Design. Current members, advisors, supporters, and old friends all came together on campus to share memories and forge new friendships. It was a night to remember. A lot has changed in the past decade. At our founding, the concept of protein design …

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Anindya Roy wins Go-To-Market Award for drug development

The Washington Entrepreneurial Research Evaluation and Commercialization Hub (WE-REACH) is pleased to announce a product concept award for Dr. Anindya Roy and his team at the UW Medicine Institute for Protein Design, including Drs. Jake Kraft and Hua Bai. They are developing a novel binder protein in an aerosolized delivery system to treat idiopathic pulmonary …

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Rotory proteins designed from scratch

Today we report in Science the design of rotary devices made from custom proteins. These microscopic “axles” and “rotors” come together to form spinning assemblies, rather than being locked in just one orientation. Such mechanical coupling is a key feature of any machine. The new axle-rotor devices — which are each about a billion times …

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Protein drugs designed from the ground up

Today we report in Nature a new method for generating protein drugs. Using Rosetta-based design, an international team designed molecules that can target important proteins in the body, such as the insulin receptor, as well as proteins on the surface of viruses. This solves a long-standing challenge in drug development and may lead to new treatments for …

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Diverse protein assemblies by (negative) design

A new approach for creating custom protein complexes yields asymmetric assemblies with interchangeable parts. Today we report in Science the design of new protein assemblies made from modular parts. These complexes — which adopt linear, branching, or closed-loop architectures — contain up to six unique proteins, each of which remains folded and soluble in the absence …

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Breakthrough of the Year

The journal Science has selected artificial intelligence algorithms that predict the three-dimensional shapes of proteins — as well as the blizzard of protein structures they have revealed — as their 2021 Breakthrough of the Year. We are honored to have our work in this field recognized alongside that of the company DeepMind. As David Baker told …

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Deep learning dreams up new protein structures

Just as convincing images of cats can be created using artificial intelligence, new proteins can now be made using similar tools. In a new report in Nature, we describe the development of a neural network that “hallucinates” proteins with new, stable structures. “For this project, we made up completely random protein sequences and introduced mutations …

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UW BIOFAB: a force for reproducible science

This article was written by Renske Dyedov (UW) Key to advancing any new scientific discovery is the ability for researchers to independently repeat the experiments that led to it. In science today, particularly biology, the lack of reproducibility between experiments is a major problem that slows scientific progress, wastes resources and time, and erodes the …

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Deep learning reveals how proteins interact

A team led by scientsts in the Baker lab has combined recent advances in evolutionary analysis and deep learning to build three-dimensional models of how most proteins in eukaryotes interact. This breakthrough has significant implications for understanding the biochemical processes that are common to all animals, plants, and fungi. This open-access work appears in Science. …

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Dr. Berger wins additional WRF translational funding

Washington Research Foundation (WRF) has awarded a $700,000 phase three technology commercialization grant to Stephanie Berger, Ph.D., to support the development of an oral biologic for inflammatory bowel disease (IBD). Berger, a translational investigator at the Institute for Protein Design, received two previous grants totaling $300,500 from WRF for this work. IBD affects roughly three …

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On the passing of Tachi Yamada

Tadataka “Tachi” Yamada MD, KBE served as the Advisory Board Chair of our Institute since its founding almost ten years ago. His tremendous mentorship helped us in innumerable ways to grow from a single-PI Institute founded by David Baker to a group of five faculty and almost 200 scientists and staff.   Tachi also helped …

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Dr. Roy awarded WRF translational funding

Washington Research Foundation (WRF) has awarded a $250,000 phase 2 technology commercialization grant to Anindya Roy, Ph.D., to further develop a novel miniprotein binder for the treatment of idiopathic pulmonary fibrosis (IPF). Roy, an acting instructor in David Baker’s lab at the University of Washington’s Institute for Protein Design (IPD), is building on positive results …

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Two nanoparticle vaccines enter clinical trials

Two different candidate vaccines developed by researchers at the Institute for Protein Design recently entered human clinical trials. GBP510, a candidate COVID-19 vaccine, is undergoing a combined Phase 1/2 trial. Flu-Mos-v1, a candidate mosaic influenza vaccine, is undergoing Phase 1 testing. Candidate COVID-19 vaccine Our SARS-CoV-2 vaccine candidate was created with structure-based vaccine design techniques …

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Drs. Ueda and Lazarovits awarded WRF translational funding

The Washington Entrepreneurial Research Evaluation and Commercialization Hub (WE-REACH) has announced investments in three new awards, including one to researches at the Institute for Protein Design, to expedite early-stage product development for promising biomedical innovations. The three awards are intended to reduce skin injury from wound dressing, to treat COVID-19 induced viral sepsis, and to …

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Companion proteins enhance antibody potency

This week we report the design of new proteins that cluster antibodies into dense particles, rendering them more effective. In laboratory testing, such clustered antibodies neutralize COVID-19 pseudovirus, enhance cell signaling, and promote the growth of T cells more effectively than do free antibodies. This new method for enhancing antibody potency may eventually be used …

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A deep learning approach to protein design

Scientists at the IPD and Ovchinnikov lab at Harvard have applied deep learning to the challenge of protein design, yielding a new way to quickly create protein sequences that fold up as desired. This breakthrough has broad implications for the development of protein-based medicines and vaccines. Computational protein design has primarily focused on finding amino …

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trRosetta yields structures for every protein family

The field of protein structure prediction has greatly advanced in recent years thanks to increasingly accurate deep-learning methods. A new such method, called trRosetta developed at the Institute for Protein Design, has now made thousands of protein structures available via EMBL-EBI’s Pfam and InterPro data resource. More than 6300 protein structures have been predicted in this way and are …

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Design of transmembrane beta barrels

Biochemists have created barrel-shaped proteins that embed into lipid membranes, expanding the bioengineering toolkit. In a milestone for biomolecular design, a team of scientists has succeeded in creating new proteins that adopt one of the most complex folds known to molecular biology. These designer proteins were shown in the lab to spontaneously fold into their …

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Dr. Berger awarded WRF translational funding

Washington Research Foundation (WRF) has provided a $250,000 grant to support work carried out by Stephanie Berger, Ph.D., on a new therapeutic for patients with inflammatory bowel disease (IBD). A grant of $50,500 from WRF in 2019 and an award from Washington Entrepreneurial Research Evaluation and Commercialization Hub (WE-REACH) in 2020 enabled Berger, a translational investigator at the …

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Protein patches boost cell signaling

Today we report the design of a new class of protein material that interacts with living cells without being absorbed by them. These large, flat arrays built from multiple protein parts can influence cell signaling by clustering and anchoring cell surface receptors. This breakthrough could have far-reaching implications for stem cell research and enable the …

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David Baker awarded 2021 Breakthrough Prize

The Breakthrough Prize Foundation today announced the winners of the 2021 Breakthrough Prize, recognizing an array of achievements in the Life Sciences, Fundamental Physics and Mathematics. The traditional gala award ceremony, attended by superstars of movies, music, sports and tech entrepreneurship, has been postponed until March 2021. David Baker, director of the Institute for Protein …

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De novo nanoparticles as vaccine scaffolds

IPD researchers have developed a new vaccine design strategy that could confer improved immunity against certain viruses, including those that cause AIDS, the flu, and COVID-19. Using this technique, viral antigens are attached to the surface of self-assembling, de novo designed protein nanoparticles. This enables an unprecedented level of control over the molecular configuration of the resulting …

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Dr. Berger selected for WE-REACH funding

  The Washington Entrepreneurial Research Evaluation and Commercialization Hub (WE-REACH) has announced its first awards to facilitate early-stage product development for two biomedical innovations. WE-REACH invests up to $200,000 per awarded project. Funding comes from the NIH with matching support from our partners at the Institute of Translational Health Sciences, CoMotion, the Institute for Protein …

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Rosetta Commons Black Lives Matter Statement

Trigger warning: mentions acts of violence and racism We, as members of the Rosetta Commons, recognize the grief and frustration of many members of our community and reaffirm our commitment to the safety and dignity of Black lives. The past few months have been traumatic. The recent murders of George Floyd, Breonna Taylor, Tony McDade, …

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Introducing UWARN: The United World Antiviral Research Network

The newly formed United World Antiviral Research Network (UWARN) will bring together researchers from institutions in several countries to spot and confront emerging pandemic viruses. The network will provide surveillance for emerging pandemic viruses, develop urgently needed diagnostics and therapeutics, and expand understanding of viral immune responses, which is key to vaccine development. The network will …

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De novo design of protein logic gates

The same basic tools that allow computers to function are now being used to control life at the molecular level, with implications for future medicines and synthetic biology.  Together with collaborators, we have created artificial proteins that function as molecular logic gates. These tools, like their electronic counterparts, can be used to program the behavior …

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Designing shape-shifting proteins

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. In nature, many proteins change shape in response to their environment. This plasticity is often linked to biological function. While computational …

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Play Foldit to help stop coronavirus (VIDEO)

You don’t have to be a scientist to do science! By playing the computer game Foldit, you can help discover new antiviral drugs that might stop the novel coronavirus. The most promising solutions will be manufactured and tested at the University of Washington Institute for Protein Design in Seattle. Foldit is run by academic research scientists. It is free …

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Introducing WE-REACH, a new biomedical innovation hub

With $4 million in matching funds from the National Institutes of Health, the University of Washington has created a new integrated center to match biomedical discoveries with the resources needed to bring innovative products to the public and improve health. “The University of Washington and regional partner institutions produce some of the most exciting biomedical …

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SCI-STEM Symposium 2020

The Institute for Protein Design at the University of Washington held the second symposium aimed at providing strategies to address diversity challenges in science, technology, engineering, and math (STEM). The Strategies for Cultivating Inclusion in STEM (SCI-STEM) symposium featured leading keynote speakers, panel discussions, and interactive breakout sessions. Members of the STEM community at all …

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Radhika wins poster award at ABRCMS!

Undergraduate researcher Radhika Dalal took home a poster award at this year’s Annual Biomedical Research Conference for Minority Students in Anaheim, California. Her mentors include IPD graduate student Una Natterman and Quinton Dowling. Way to go Radhika! And congratulations to all the award winners:

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Icosavax launches to advance designer vaccines

Icosavax, Inc. today announced its launch with a $51 million Series A financing. The company was founded on computationally designed self-assembling virus-like particle (VLP) technology developed here at the IPD (Cell 2019, Preview). The proceeds of the financing will be used to advance the company’s first vaccine candidate, IVX-121, for respiratory syncytial virus (RSV) for …

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Neoleukin: from spinout to public company in 7 months

IPD-spinout Neoleukin Therapeutics announced this week a merger with Aquinox Pharmaceuticals, a publicly traded company. The combined company will change its name to Neoleukin Therapeutics, and will continue to advance its Rosetta-designed protein platform for cancer, inflammation, and autoimmune diseases. Neoleukin was spun out of the IPD Translational Investigator Program in January. As a result …

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5 questions about LOCKR from our Reddit AMA

Researchers from the IPD and UCSF recently participated in a Reddit Ask Me Anything about LOCKR, our new de novo protein switch. Reddit users had dozens of fantastic questions — so many, in fact, that the team ran out of time before they could address them all. “The questions were both insightful and interesting,” says …

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Introducing LOCKR: a bioactive protein switch

Today we report in Nature the design and initial applications of the first completely artificial protein switch that can work inside living cells to modify—or even commandeer—the cell’s complex internal circuitry. The switch is dubbed LOCKR, short for Latching, Orthogonal Cage/Key pRotein. “In the same way that integrated circuits enabled the explosion of the computer chip industry, these versatile and dynamic …

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Coevolution at the proteome scale

Today we report in Science the identification of hundreds of previously uncharacterized protein–protein interactions in E. coli and the pathogenic bacterium M. tuberculosis. These include both previously unknown protein complexes and previously uncharacterized components of known complexes. This research was led by postdoctoral fellow Qian Cong and included former Baker lab graduate student Sergey Ovchinnikov, now a John Harvard Distinguished Science …

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Protein arrays on mineral surfaces

Today we report the design of synthetic protein arrays that assemble on the surface of mica, a common and exceptionally smooth crystalline mineral. This work, which was performed in collaboration with the De Yoreo lab at PNNL, provides a foundation for understanding how protein-crystal interactions can be systematically programmed. Our goal was to engineer artificial proteins to self-assemble on …

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Protein design by citizen scientists

Citizen scientists can now use Foldit to successfully design synthetic proteins. The initial results of this unique collaboration appear today in Nature. Brian Koepnick, a recent PhD graduate in the Baker lab, led a team that worked on Foldit behind the scenes, introducing new features into the game that they believed would help players home in on …

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Designed ligands tune cytokine signaling

Today the Baker lab shares some exciting collaborative results of their efforts to design rigid and tunable receptor dimerizers. The first authors of this report are Kritika Mohan, Stanford, and George Ueda, IPD. From Science: Exploring a range of signaling Cytokines are small proteins that bind to the extracellular domains of transmembrane receptors to activate signaling pathways …

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Tunable pH-dependent assemblies

Natural proteins often shift their shapes in precise ways in order to function. Achieving similar molecular rearrangements by design, however, has been a long-standing challenge. Today, a team of researchers lead by scientists at the IPD report in Science the rational design of synthetic proteins that move in response to their environment in predictable and tunable …

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Receptor sub-type binders

This week we report in NSMB a combined computational design and experimental selection approach for creating proteins that bind selectively to closely related receptor subtypes. This project was led by Luke Dang, a former Baker lab graduate student, and Yi Miao, a postdoctoral researcher in Christopher Garcia’s lab at Stanford. Abstract: To discriminate between closely related members of …

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De novo 2D arrays

This week we report in JACS a general approach for designing self-assembling 2D protein arrays. This project was led by Zibo Chen, a recent Baker lab graduate student, and featured collaborators from the, DiMaio, De Yoreo and Kollman labs at UW. Abstract: Modular self-assembly of biomolecules in two dimensions (2D) is straightforward with DNA but …

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Our outstanding postdoc mentors

Each year, a panel here at the University of Washington nominates a small number postdocs of the UW Graduate School’s Postdoc Mentoring Award. We are thrilled to share that this year four of our postdocs have been nominated! Each brings invaluable encouragement and advice to their graduate student and undergraduate trainees. Winner: Gabriella Wolff, Biology Finalists: Michael Beyeler, …

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Our Audacious Project

Yesterday we were thrilled to reveal that we have been selected as part of The Audacious Project, a philanthropic collaborative organized by TED! You can read all about our project here. In short, we are expanding our institute into a global hub of innovation so that we can apply protein design to some of the …

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IPD’s first nanoparticle vaccine

Today we report in Cell our first computer-designed nanoparticle vaccine targeting respiratory syncytial virus (RSV). Millions of children will visit hospitals this year, sickened by RSV. Infection is usually mild, causing only fevers, runny noses and frightened parents. But, in severe cases, barking coughs and painful wheezing can indicate serious respiratory complications, including bronchiolitis and …

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Potent anti-cancer proteins with fewer side effects

Today we report in Nature the first de novo designed proteins with anti-cancer activity. These compact molecules were designed to stimulate the same receptors as IL-2, a powerful immunotherapeutic drug, while avoiding unwanted off-target receptor interactions. We believe this is just the first of many computer-generated cancer drugs with enhanced specificity and potency. “People have tried for 30 …

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New designer proteins mimic DNA

To close out the year, Baker Lab scientists published a new report describing the creation of proteins that mimic DNA. We believe this breakthrough will aid the creation of bioactive nanomachines. DNA is a widely used building material at the nanoscale because it is simple and predictable: A pairs with T and C pairs with …

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Rolling out new jellies

The basic parts of proteins — helices, strands and loops — can be combined in countless ways. But certain combinations are trickier than others. This week scientists from the IPD, along with collaborators in Brno and Santa Cruz, published the first-ever example of designed non-local beta-strand interactions. Beta-sheet proteins carry out critical functions in biology, …

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2018 IPD Newsletter from David Baker

It was a great year for the Institute for Protein Design and we couldn’t have done all of our amazing work without the support from our donors and contributors! Thank you to everyone who helped us, whether through a donation, collaboration, playing Foldit, or otherwise. We’ve filled the IPD Newsletter with all of the progress …

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Open Philanthropy Project Awards $11.3 Million to Institute for Protein Design at UW Medicine

Graphic: Possu Huang

Gift seeks universal flu vaccine and will advance Rosetta software         Seattle — The Institute for Protein Design (IPD) at UW Medicine in Seattle has been awarded $11.3 million from the Open Philanthropy Project to support the institute’s technological revolution in protein design and support its work on the development of a universal flu vaccine. The …

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SCI-STEM Symposium 2018

Update 2018-07-26: The 2018 SCI-STEM Symposium was recently featured in an eLife article. The Institute for Protein Design at the University of Washington held its first ever symposium aimed at providing strategies to address diversity challenges in science, technology, engineering, and math (STEM). The Strategies for Cultivating Inclusion in STEM (SCI-STEM) symposium featured leading keynote …

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De Novo Design of Membrane Proteins

It is now possible to create complex, custom-designed transmembrane proteins from scratch !   Today Baker lab members published in Science  “Accurate computational design of multipass transmembrane proteins” The Abstract reads as follows: The computational design of transmembrane proteins with more than one membrane-spanning region remains a major challenge. We report the design of transmembrane monomers, …

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End-of-year profile in The New York Times

At the end of a historic year for protein design, the Baker lab was honored to be profiled in the New York Times by famed science writer Carl Zimmer. Zimmer writes about the technology, progress and promise in the field, noting the contributions from our wonderful crowdsource participants. Graphic: John Hersey / New York Times On the technology front, …

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A New World of Designed Macrocycles

Today marks another major step forward for peptide based drug discovery.  IPD researchers report in Science the computational design of a new world of small cyclic peptides, “Macrocycles”,  increasing the number of the known kinds of these molecules by multiple fold.  The conceptual art image below “Illuminating the energy landscape” shows the power of computational design …

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Synthetic Nucleocapsids Have Arrived

Published today in Nature, IPD researchers describe the first synthetic protein assemblies — dubbed synthetic nucleocapsids — that encapsulate their own genome and evolve in complex environments. Synthetic nucleocapsids are built to resemble viral capsids and could be used in future to deliver therapeutics to specific cells and tissues. These icosahedral protein assemblies are based off of …

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Foldit to Disarm a Fungal Toxin

Foldit alfatoxin project update 7/16/2018 Today, scientists from of the Institute for Protein Design will join Foldit gamers from around the world to help design an enzyme that can neutralize aflatoxin — a cancer-causing toxin produced by certain fungi that are found on agricultural crops such as corn, peanuts, cottonseed, and tree nuts.  Foldit is a citizen …

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Designs on New World of Mini-Protein Therapeutics

Mark your calendars!  September 27, 2017 is the day the doors opened to whole new world of targeted therapeutics.  The Baker lab and numerous talented collaborators published in Nature that it is now possible to conduct “Massively parallel de novo protein design for targeted therapeutics”.  Three factors make this possible: Rosetta molecular modeling algorithms for computational protein …

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2017 IPD Newsletter from David Baker

It was a great year for the Institute for Protein Design and we couldn’t have done all of our amazing work without the support from our donors and contributors! Thank you to everyone who helped us, whether through a donation, collaboration, playing Foldit, or otherwise. We’ve filled the IPD Newsletter with all of the progress …

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Cyrus Raises $8M to Advance Cloud-Based Protein Modeling and Design

Today, the first IPD spin out company Cyrus Biotechnology announced the closing of an $8M total Series A financing. The investment was led by Trinity Ventures, with participation from OrbiMed Advisors, SpringRock Ventures, W Fund, WRF Capital (a major supporter of the IPD), and individual investors.   Congratulations  Cyrus team! Cyrus is commercializing Cyrus Bench® an innovative user friendly software as …

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Arzeda Raises $12M for Computational Protein Design

Today, Baker lab spin out company Arzeda announced that it had raised $12 million in a Series A round of funding led by OS Fund and including Bioeconomy Capital and Sustainable Conversion Ventures, as well as a follow-on investment from Arzeda’s seed investor, WRF Capital (a major supporter of the IPD).  The new funding will enable “Technology …

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The Matrix of Protein Design

The Matrix movie (1999) depicts a future in which the reality perceived by most humans is actually a computer simulated reality called “the Matrix”.  Published today in Science, the Baker lab and collaborators report on a new kind of Matrix –  a new reality for large scale computational protein design which can achieve massive data driven improvements in our ability to design highly stable, …

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Stopping Influenza with Flu-Glue

Today, a multidisciplinary team of researchers at the University of Washington, Fred Hutch, and The Scripps Research Institute published in Nature Biotechnology the computational design of a trimeric influenza-neutralizing protein that binds extremely tightly to the H3 hemagglutinin of 1968 Hong Kong pandemic influenza virus (A/Hong Kong/X31/1968). It also cross-reacts with human relevant H1, H2 and …

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Thank you, Bruce and Jeannie Nordstrom!

A few months ago, it was announced that the Institute for Protein Design is one of UW Medicine’s Priorities in their ACCELERATE campaign. We are grateful to have this support not only from UW Medicine, but also from donors who are contributing funds so that we may continue our work. One such gift came from …

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Design of novel cavity containing proteins

The latest paper coming out from the IPD was published today on the Science website. It’s titled “Principles for designing proteins with cavities formed by curved β sheets” with first co-authors Enrique Marcos and Benjamin Basanta, a former and current IPD member, respectively. Other IPD members on the paper include Tamuka Chidyausiku, Gustav Oberdorfer, Daniel-Adriano …

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New spinout: PvP Biologics!

We are happy to congratulate Ingrid Swanson Pultz, an IPD Translational Investigator, and Clancey Wolf, a Research Scientist, on PvP Biologics‘ spinout! The news was announced this morning and has been circulated through various outlets. The company, created in 2015, is focusing on advancing KumaMax, a gluten-fighting enzyme that could potentially be taken orally to …

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Arzeda Scales its Automated Molecule Development Pipeline

Seattle-based Arzeda, a computational and synthetic biology company that was spun out from the University of Washington labs of Prof. David Baker, recently announced that its high-throughput, automated pipeline for protein engineering and pathway discovery had been validated by the production of two keystone molecules. The announcement is a major technical milestone for Arzeda’s approach …

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Unleashing the Power of Synthetic Proteins

Published today in Science Philanthropy Alliance,  David Baker, Director of the Institute for Protein Design describes how the opportunities for computational protein design are endless — with new research frontiers and a huge variety of practical applications to be explored, from medicine to energy to technology. This is an exciting time as we are undergoing a technological revolution …

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Hyper-stable Designed Peptides and the Coming of Age for De Novo Protein Design

Small constrained peptides combine the stability of small molecule drugs with the selectivity and potency of antibody-based therapeutics. However, peptide-based therapeutics have largely remained underexplored due to the limited diversity of naturally occurring peptide scaffolds, and a lack of methods to design them rationally.  New computational design and wet lab methods developed at the Institute for …

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