Institute for Protein Design

August 7, 2015

July IPD News Roundup


It’s been a hot summer in Seattle so far! IPD scientists and staff have been enjoying the sun but also welcoming some new visitors and a new IPD faculty member. More at the link.

July 7, 2015

June IPD News Roundup

P-icon-colorJune was a very exciting month at the IPD. We launched our first company spinout, published a Science paper on two-dimensional protein arrays, and more. Read on at the link!

June 23, 2015

New Science paper: Designed 2-D protein arrays

A new Science paper is out from IPD faculty Dr. David Baker titled Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces. Read the abstract below and the article at the link:

We describe a general approach to designing two-dimensional (2D) protein arrays mediated by noncovalent protein-protein interfaces. Protein homo-oligomers are placed into one of the seventeen 2D layer groups, the degrees of freedom of the lattice are sampled to identify configurations with shape-complementary interacting surfaces, and the interaction energy is minimized using sequence design calculations. We used the method to design proteins that self-assemble into layer groups P 3 2 1, P 4 2(1) 2, and P 6. Projection maps of micrometer-scale arrays, assembled both in vitro and in vivo, are consistent with the design models and display the target layer group symmetry. Such programmable 2D protein lattices should enable new approaches to structure determination, sensing, and nanomaterial engineering.


Shown is a 2D array with P 6 symmetry. (Left) the P 6 lattice has two degrees of freedom available for sampling. Sixfolds are represented by hexagons. (Middle) Computationally designed 2D array. (Right) Electron microscopy of designed P 6 array.

June 2, 2015

IPD Launches First Company Spinout

Cyrus_thumbnailThe IPD is thrilled to announce its first company spinout today – Cyrus Biotechnology! Cyrus aims to pursue commercialization of an innovative user friendly software as a service (SaaS) cloud computing solution for distribution of the powerful “Rosetta” protein structure prediction and design algorithms. Read our press release about exciting startup at this link.

June 1, 2015

May IPD News Roundup

P-icon-colorThe May IPD News Roundup covers a new Science paper from IPD Assistant Prof Frank DiMaio, a KOMO News interview with Translational Investigator Ingrid Swanson Pultz on celiac disease, and much more! At the link.

May 31, 2015

New structure solved for hyperthermophilic DNA virus

A new Science paper is out from IPD faculty Dr. Frank DiMaio titled A virus that infects a hyperthermophile encapsidates A-form DNA. Read the abstract below and the article at the link:

Extremophiles, microorganisms thriving in extreme environmental conditions, must have proteins and nucleic acids that are stable at extremes of temperature and pH. The nonenveloped, rod-shaped virus SIRV2 (Sulfolobus islandicus rod-shaped virus 2) infects the hyperthermophilic acidophile Sulfolobus islandicus, which lives at 80°C and pH 3. We have used cryo–electron microscopy to generate a three-dimensional reconstruction of the SIRV2 virion at ~4 angstrom resolution, which revealed a previously unknown form of virion organization. Although almost half of the capsid protein is unstructured in solution, this unstructured region folds in the virion into a single extended a helix that wraps around the DNA. The DNA is entirely in the A-form, which suggests a common mechanism with bacterial spores for protecting DNA in the most adverse environments.


The SIRV2 protein dimer helices fully encapsulate the DNA. (A) Three asymmetric units of the virion are shown, illustrating how the N-terminal helices wrap around the DNA, forming antiparallel helix-helix packing. (B) Side view. (C) Surface view of the protein (using a 1.4 Å probe radius). (D) The right-handed solenoidal supercoiling of the DNA, with three turns shown.



April 13, 2015

March IPD News Roundup

P-icon-colorThe March 2015 IPD news roundup is here! A new publication in PNAS on a completely novel metabolic pathway made via protein design and more. Read about it at the link.

March 12, 2015

February IPD News Roundup

Screen Shot 2015-03-12 at 9.06.15 AMThis month’s roundup features an interview and two papers from IPD Assistant Professor Frank DiMaio as well as a new Science paper from the Baker lab on trapping transition states using protein design. Read more at the link.

February 25, 2015

AAAS 2015 Plenary Lecture by David Baker

David Baker, IPD Director and Professor of Biochemistry at the UW was the Plenary Speaker at this year’s AAAS meeting in San Francisco. A video of his talk, titled ‘Post-Evolutionary Biology: Design of Novel Protein Structures, Functions, and Assemblies’ covers a breadth of information on ongoing IPD research and can be viewed at the following link:

February 18, 2015

January IPD News Roundup

P-icon-colorA little late this month but it’s here!!! The January news roundup talks about a new Nature journal paper from the Baker lab, the second Mini Symposium, and much more. Follow the link and read more!

January 27, 2015

Independent Study Opportunity for Foster MBA Students

foster_iconThe Institute for Protein Design is seeking an MBA student to work with Institute leadership to collect market data on small molecule therapeutic targets for protein design. More information about this exciting independent study opportunity can be found on our Employment page here.

January 12, 2015

IPD Mini Symposium – Jan 20 2015

P-icon-colorOur next Mini Symposium will be hosted on Jan 20 2015 and will feature Drs. Bill DeGrado (UCSF) and Gevorg Grigoryan (Dartmouth) speaking on “New Approaches to Protein Design”. More information at this link.

January 6, 2015

December IPD News Roundup

P-icon-colorWe wrapped up 2014 with a bang – introducing a new logo, getting a major award for celiac disease research, and successfully hosting our first Mini Symposium! Follow the link to read more.

December 15, 2014

Translational Investigator awarded LSDF Matching Grant Award for Celiac Disease Therapy

Ingrid Swanson-PultzSlide18







Please make a tax deductible donation at this LINK. 

IPD Translational Investigator Dr. Ingrid Swanson Pultz was awarded a Matching Grant award of $250K from the Life Sciences Discovery Fund (LSDF) for her project ‘In vivo assessment of an oral therapeutic for celiac disease‘!

We need to raise an additional $74K to make the full match.

Learn more about this project by watching this short  video.

For more information, watch this longer WBBA video, interview with Ingrid, and look this slide presentation.

The goal of this LSDF funded research is to assess the efficacy, safety, and optimal dosing of KumaMax and its variants as an oral enzyme therapy for celiac disease.

KumaMax is the winner of the 2013 Innovation Award at the UW.   KumaMax is a computationally designed enzyme which efficiently breaks down gluten in the stomach before it reaches the small intestine where it can cause inflammation in celiac disease patients.

The LSDF Matching Grant has the requirement that the UW must raise an additional 1:1 match of $250K to support this innovative project.

We need your support !  The Institute for Protein Design has received $176K in matching funds from generous philanthropists to support this work.

Every $ counts.  We thank everyone for their generous support.


December 2, 2014

November IPD News Roundup

Twitter_UWproteindesignStaff and scientists of the IPD and Foldit volunteered at Pacific Science Center’s Life Sciences Research Weekend this month – teaching budding scientists about the awesomeness of protein folding! Pics from the event and more Institute news at the link.

December 1, 2014

IPD Mini Symposium 2014

The UW Institute of Protein Design (IPD) presents a Mini Symposium on “Sweet Spots for Designed Proteins as Therapeutics” on Weds Dec 10 at 9 AM in HSB D-209. Follow the link to get more details! We hope to see you there!


November 3, 2014

October IPD News Roundup

October News RoundupHappy Fall from the IPD! Read about our October happenings in this month’s news roundup. Click here to read more.

October 24, 2014

Custom design of novel alphahelical bundles

Three helix bundle thumbnailA new paper is out in this week’s issue of Science entitled High thermodynamic stability of parametrically designed helical bundles. Using novel computational design methods, extremely stable helical bundles can be custom designed with fine-tuned structural geometries for a number of applications. Read more about this exciting work at this link.

October 1, 2014

September IPD News Roundup

SeptNewsRoundupWe awarded our first round of WRF Innovation Postdoctoral fellowships this month! Follow the link to learn about our new fellows and to catch up on the research ongoing at the IPD.

September 2, 2014

August IPD News Roundup

Twitter_UWproteindesignThe Foldit community has been leading the charge in the computational design of proteins to bind Ebola. Learn more about this work and other ongoing Institute news at the link.

August 28, 2014

Engineering an Oral Therapeutic for Celiac Disease

Slide18Learn how the IPD and Translational Investigator Dr. Ingrid Swanson Pultz are developing Kumamax, an oral therapeutic candidate for celiac disease. A slide presentation and more information at the link.

July 31, 2014

July IPD News Roundup

This July, IPD staff and scientists ventured outdoors for a conference and for some fun adventures. Learn more at the link.Twitter_UWproteindesign

June 30, 2014

June IPD News Roundup

Twitter_UWproteindesignJune at the IPD welcomed some new team members and saw some exciting new publications! Learn more here.

June 19, 2014

Designer Proteins to Target Cancer Cells

BINDI Designer Protein What if scientists could design a completely new protein that is precision-tuned to bind and inhibit cancer-causing proteins in the body? Collaborating scientists at the UW Institute for Protein Design (IPD) and Molecular Engineering and Sciences Institute (MolES) have made this idea a reality with the designed protein BINDI. BINDI (BHRF1-INhibiting Design acting Intracellularly) is a completely novel protein, based on a new protein scaffold not found in nature, and designed to bind BHRF1, a protein encoded by the Epstein-Barr virus (EBV) which is responsible for disregulating cell growth towards a cancerous state. Learn more here.

June 4, 2014

Accurate Design of Co-Assembling Multi-Component Protein Nanomaterials

TwoComponentthumbnailA new paper is out in the June 5 issue of Nature entitled Accurate design of co-assembling multi-component protein nanomaterials. Scientists at the Institute for Protein Design (IPD), in collaboration with researchers at UCLA and HHMI, have built upon their previous work constructing single-component protein nanocages and can now design and build self-assembling protein nanomaterials made up of multiple components with near atomic-level accuracy. Learn more about this innovative work at this link.

May 30, 2014

May IPD News Roundup

Twitter_UWproteindesignMay was a busy month at the IPD, with some new publications and exciting announcements! Learn more here.

May 22, 2014

Removing T-cell Epitopes with Computational Protein Design

King_2014AIn a recent PNAS paper entitled “Removing T-cell epitopes with computational protein design”, IPD researchers combine machine learning with computational protein design to demonstrate immune silencing of protein targets. This deimmunization has the potential to reduce or eliminate immunogenicity of protein therapeutics. Learn more at this link.

May 19, 2014

Women in Science Lunch Discussion

Women in Science lunch_smallA recent Nature issue exposed the dismaying fact that many women are deterred from pursuing a career in science, especially at the highest levels (postdoctoral positions, faculty position, scientific advisory boards to start up companies, etc). To talk about this significant gender gap in science and the issues female scientists face, Baker lab members participated in an informal lunch discussion to determine what specific steps could be taken as a group to encourage and promote women within our own scientific community. Learn more at this link.

May 15, 2014

WRF Awards $8M for the IPD Innovation Fellows Program

WRF LogoWith a very generous $8 M gift from the Washington Research Foundation (WRF), the IPD has launched the WRF-IPD Innovation Fellows Program supporting research partnerships between the IPD and other Seattle-area research institutes or UW departments.  We are recruiting exceptionally talented researchers who have just finished their PhD to join expert laboratories at local institutions where they will apply protein design methods to current health, energy, and materials related research problems.  For more information see our web page here

April 23, 2014

Beyond Evolution: Protein Design News and Art

Flu BinderRe/Code writer James Temple has written an interesting article on David Baker’s efforts to design a new world of proteins.  The article covers the IPD efforts to design proteins that neutralize the flu virus, Alzheimer’s disease amyloid protein, and how the IPD is engaging citizen scientists in the Rosetta@home and Foldit projects.  Learn more at this link.

April 6, 2014

Design of Activated Serine-Containing Catalytic Triads with Atomic-Level Accuracy

Catalytic Serine TriadBaker lab members published in Nature Chemical Biology a paper entitled “Design of activated serine-containing catalytic triads with atomic-level accuracy“, describing the computational design of proteins with idealized serine-containing catalytic triads which can capture and neutralize organophosphate probes.  This work has utility in design of scavengers of environmental toxins. Learn more at this link.

February 14, 2014

A Computationally Designed Metalloprotein Using an Unnatural Amino Acid

Mulligan metal binder figureWhat if scientists could design proteins to capture specific metals from our environment?  The utility for cleaning up metals from waste water, soils, and our bodies could be tremendous.  Dr. Jeremy Mills and collaborators in Dr. Baker’s group at the University of Washington’s Institute for Protein Design (IPD) address this challenge in the first reported use of computational protein design software, Rosetta, to engineer a new metal binding protein (“MB-07”) which incorporates an “unnatural amino acid” (UAA) to achieve very high affinity binding to metal cations.  Learn more at this link.

January 1, 2014

Computational Design of a pH Sensitive Antibody Binder

Designed pH-dependent Fc binder (blue) exploits protonation of Histidine-433 (orange) in the Fc portion Immunoglobulin G (IgG, light cyan surface)

Purification of antibody IgG from crude serum or culture medium is required for virtually all research, diagnostic, and therapeutic antibody applications.  Researchers at the Institute for Protein Design (IPD) have used computational methods to design a new protein (called “Fc-Binder”) that is programed to bind to the constant portion of IgG (aka “Fc” region) at basic pH (8.0) but to release the IgG at slightly acidic pH (5.5).  Published on-line at PNAS (Dec. 31, 2013), the paper is entitled Computational design of a pH-sensitive IgG binding protein, co-authored by Strauch, E. – M., Fleishman S. J., & Baker D.  Learn more at this link.

December 16, 2013

KumaMax: Winner of C4C Recognition as a Novel Oral Therapeutic for Celiac Disease


Dr. Ingrid Swanson Pultz wins first prize at C4C's 2013 Innovators Recognition Event

Dr. Ingrid Swanson Pultz, a Translational Investigator at the Institute for Protein Design won first prize at the UW Center for Commercialization 2013 Innovator Recognition Event, for KumaMax, an enzyme designed in the Baker lab to efficiently break down gluten within the acidic environment of the stomach, before it can reach the small intestine where intact gluten may otherwise cause an inflammatory reaction in people who suffer from celiac disease.  Learn more at this link.

November 15, 2013

Computational Protein Design To Improve Detoxification Rates Of Nerve Agents

Phosphotriesterase EngineeringV-type nerve agents are among the most toxic compounds known, and are chemically related to pesticides widespread in the environment. Using an integrated approach, described in an ACS Chemical Biology paper entitled Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries, Dr. Izhack Cherny, Dr. Per Greisen, and collaborators increased the rate of nerve agent detoxification by the enzyme phosphotriesterase (PTE) by 5000-fold by redesigning the active site.   Learn more at this link.

October 23, 2013

Institute for Protein Design Infograph

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October 8, 2013

High-Resolution Comparative Modeling with RosettaCM

RosettaCMResearchers in the Baker group describe an improved method for comparative modeling, RosettaCM, which optimizes a physically realistic all-atom energy function over the conformational space defined by homologous structures.  Learn more at this link.

September 16, 2013

Life Sciences Discovery Fund Awards $1.4M to the Institute for Protein Design

LSDFThe Life Sciences Discovery Fund  (LSDF) today announced its latest round of Opportunity Grants, and awarded $1.4 M to the University of Washington (UW) to “Launch of the Institute for Protein Design for Creating New Therapeutics, Vaccines and Diagnostics.”   This LSDF Opportunity Grant Award will enable the IPD Translational Investigators to improve upon protein design discoveries so that they may one day become viable solutions to real-life challenges.  UPDATE April 2014: The LSDF funding to the IPD was matched 4-fold by generous contributions from private donors ($3.2 M), UW ($1.4 M), and the Washington Research Foundation ($1 M).  Learn more at this link.

April 2, 2013

IPD Researchers Publish New Protocols for Preparing Protein Scaffold Libraries for Functional Site Design

Pareto-optimal refinementIPD researchers in the Baker group have published new computational protocols for preparing protein scaffold libraries for functional site design.  Their paper entitled “A Pareto-optimal refinement method for protein design scaffolds improves the search for amino acids with the lowest energy subject to a set of constraints specifying function.  Learn more at this link.

December 13, 2012

Centenary Award and Frederick Gowland Hopkins Memorial Lecture

Centenary Award LectureDr. David Baker, Director of the IPD delivered the Centenary Award and Frederick Gowland Hopkins Memorial Lecture at  at the MRC Laboratory of Molecular Biology, Cambridge, UK, on December, 13, 2012.   Baker’s lecture entitled “Protein folding, structure prediction and design”  can be read at this published link.  

See:  Baker, D. (2014).  Protein folding, structure prediction and design.. Biochemical Society transactions. 42(2), 225-9.

June 1, 2012

Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy

Self Assembling NanomaterialsIPD researchers in the Baker group have published in Science a paper entitled “Computational design of self-assembling protein nanomaterials with atomic level accuracy.”  They describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture.  Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly.  Read more at this link.

April 13, 2012

UW to Establish Institute for Protein Design

IPDDr. Paul Ramsey, CEO of UW Medicine, announces the establishment of the Institute for Protein Design (IPD).   “A major challenge for designing proteins for specific purposes is predicting three-dimensional shape from the amino acid sequence. Dr. David Baker, UW professor of biochemistry and an investigator of the Howard Hughes Medical Institute, has had remarkable success in making these predictions and in designing new proteins with new functions.”  

Baker will serve as the director or the IPD which will coalesce and expand existing strengths within the UW and Seattle. The IPD will integrate UW expertise in biochemistry, engineering, computer science and medicine, and leverage local strength in the software industry to design a whole new world of synthetic proteins that address challenges in medicine, energy and technology.

See full press release and additional information at this link.