David Baker, PhD

Director, Institute for Protein Design

Investigator, Howard Hughes Medical Institute

Henrietta and Aubrey Davis Endowed Professor of Biochemistry, University of Washington

Adjunct Professor, Genome Sciences, Bioengineering, Chemical Engineering, Computer Science, and Physics, University of Washington

Faculty Page

dabaker@uw.edu

ipdadmin@uw.edu (assistant)

AllActing InstructorsGraduate StudentsPostdoctoral ScholarsResearch ScientistsUndergraduatesVisitorsLab Managers

Abbas Idris

Grad Student

Abishai Ebenezer

Research Scientist

Abishai is working on how to use deep learning for more efficient protein backbone design in RFdiffusion.

Adam Broerman

Grad Student

Adam is working out how to design the dynamics (interaction kinetics and conformational change) of protein assemblies.

Adam Chazin-Gray

Grad Student

Adam is focused on the mechanisms of antibiotic resistance and hopes to make novel antimicrobials.

Aditya Krishnakumar

Grad Student

Aditya is working on cytokine mimics (IL10 and TNF family specifically) for therapeutics.

Al Nelson, PhD

Visitor

Al is a Bernard and Claudine Nist Endowed Fellow and Associate Professor of Chemistry in the UW Department of Chemistry

Alexander Heynisch

Visitor

Alex is a visiting PhD student from the Biozentrum (University of Basel) in Switzerland.

Alexis Courbet, PhD

Research Scientist

Alexis is working to rationally install dynamic and mechanical behavior into de novo protein nanostructures.

Amijai Saragovi, PhD

Postdoc

Amijai is developing protein-guanine-based optical matter with the aim of constructing tunable reflective systems.

Amir Motmaen

Grad Student

Amir is redesigning T-cell receptors to recognize peptide-MHC antigens of interest for treatment of infectious diseases and cancer.

Andrew Favor

Grad Student

Andrew is interested in designing nanostructures with novel topologies and symmetries.

Andrew Hunt, PhD

Postdoc

Anna Lauko

Grad Student

Arvind Pillai, PhD

Postdoc

Arvind is working on the de novo design of an allosterically-regulated protein-protein interactions.

Avi Swartz

Grad Student

Avi is designing new proteins for artificial photosynthesis.

Basile Wicky, PhD

Postdoc

Basile is trying to design protein-protein interactions with tunable kinetic and thermodynamic binding profiles.

Beau Lonnquist

Undergrad

Beau is designing de novo transcription factors to regulate gene expression.

Bingxu Liu, PhD

Postdoc

Bingxu is working on exploring and overcoming the limitations of natural biological systems.

Brian Coventry, PhD

Research Scientist

Brian is designing protein-protein interactions.

Brian Koepnick, PhD

Research Scientist

Brian works on Foldit, a computer game we use to crowdsource problems in protein modeling and design.

Buwei Huang

Grad Student

Buwei is developing de novo protein binders to manipulate cell signaling and achieve ideal functions (e.g. antagonist, agonist).

Caixuan Liu, PhD

Postdoc

Caixuan is designing minibinders that contain antibody CDR loops.

Cameron Glasscock, PhD

Postdoc

Cameron is designing protein-DNA interactions.

Chan Johng Kim, PhD

Postdoc

Chan Johng is interested in designing proteins that have unique immunological and physiological properties.

Christian Richardson

Grad Student

Christian is designing synthetic nucleocapsids that can deliver nucleic acid cargo into cells.

Clara McCurdy

Grad Student

Clara is using designed proteins to study signaling and direct stem cell differentiation.

Cole A DeForest, PhD

Visitor

Cole is the Weyerhaeuser Endowed Professor of Chemical and Bioengineering at UW.

Cullen Demakis

Grad Student

Cullen is interested in enzyme design and two-state design.

David Chmielewski, PhD

Postdoc

David is developing non-viral delivery vehicles using designed nanocages.

David Juergens

Grad Student

David is interested in developing deep-learning based solutions for protein sequence and structure generation.

David Kim

Research Scientist

David is designing minibinders and beta-barrels.

David Lee

Grad Student

David is excited about understanding how cells work.

Declan Evans, PhD

Postdoc

Declan is working on computational enzyme design.

DéJenaé See

Grad Student

Derrick Hicks, PhD

Postdoc

Derrick is developing minibinder-drug conjugates.

Doug Tischer, PhD

Postdoc

Doug is exploring the use of machine learning to extract protein design rules from high-throughput screens.

Edin Muratspahic, PhD

Postdoc

Edin is designing miniprotein binders targeting GPCRs.

Ellen Shrock, PhD

Postdoc

Emily Na

Undergrad

Emily is designing new DNA-binding proteins as tools for transcriptional regulation.

Erin Yang

Postdoc

Erin is working on nanocages, targeted delivery, next-generation vaccines, and STEM outreach.

Florian Praetorius, PhD

Postdoc

Ge Liu, PhD

Postdoc

Green Ahn, PhD

Postdoc

Gyu Rie Lee, PhD

Research Scientist

Gyu Rie is designing proteins that bind to small molecules.

Han Raut Altae-Tran, PhD

Postdoc

Hannah Han

Undergrad

Hannah is designing amyloidogenic peptide traps to inhibit and degrade fibril formation in neurodegenerative diseases.

Hao Shen, PhD

Postdoc

Hao is designing new protein materials.

Harley Pyles, PhD

Research Scientist

Harley is designing and testing protein-inorganic hybrid materials.

Helen Eisenach

Grad Student

Helen is using deep-learning for the design of self-assembling protein nanomaterials.

Hernan Nunez-Ortega

Lab Manager

206-685-7127

Hojun Choi, PhD

Postdoc

Hojun is designing light-responsive proteins for optogenetic control, and fluorescent proteins with tunable emission wavelengths.

Ian Humphreys

Grad Student

Ian uses deep learning and coevolution to predict proteome-wide protein interactions and oligomeric structures.

Indrek Kalvet, PhD

Postdoc

Indrek is designing new (metallo)enzymes based on de novo protein scaffolds.

Inna Goreshnik, PhD

Research Scientist

Isaac Sappington

Grad Student

Ivan Anishchenko, PhD

Acting Instructor

Ivan is developing new methods for protein structure prediction and design including deep-learning based methods.

Jacob Gershon

Grad Student

Jacob is interested in generative modelling to address challenges in protein design.

Jason Qian, PhD

Postdoc

Jason Zhang, PhD

Postdoc

Jason is developing molecular tools for Ras signaling.

Jeremiah Sims

Grad Student

Jilliane Perkins, PhD

Postdoc

Jilliane is using designed protein switches to deliver therapeutics to cancer cells expressing a precise combination of surface antigens.

Jinwei Xu, PhD

Postdoc

Jinwei is exploring ways to integrate engineered biological macromolecules with synthetic nanomaterials.

Joe Min

Grad Student

Joe is interested in developing and applying deep learning methods to design proteins to help plants survive climate change.

Joseph Cotruvo, PhD

Visitor

Joseph is an Associate Professor of Chemistry at Penn State.

Joseph Watson, PhD

Postdoc

Joe develops generative deep learning methods for protein structure & sequence design. He co-developed RFdiffusion and RFjoint at the IPD.

Jungho Chun

Grad Student

Jungho is designing proteins that can modulate immune cells to differentiate into certain cell stages and elicit desired immune responses.

Justas Dauparas, PhD

Acting Instructor

Justas is developing machine learning methods for protein structure prediction and design.

Kandise Van Wormer

Sr. Lab Manager

206-685-7127

Karly Fear

Visitor

Karly is a visiting PhD student from the Hosseinzadeh Lab at the University of Oregon working on protein binder design.

Kathryn Shelly, PhD

Postdoc

Kathryn is designing proteins that undergo light-driven conformational change.

Kejia Wu

Grad Student

Kejia is developing methods for binding linear peptides and intrinsically disordered proteins, and exploring their functions in nature.

Kiera Sumida

Grad Student

Kiera is leveraging Rosetta and deep-learning methods to discover and design novel PET hydrolases.

Kirsten Thompson

Grad Student

Kirsten is broadly interested immunomodulation and cancer immunotherapy applications of protein design.

Laura Guerrero

Visitor

Linna An, PhD

Postdoc

Linna designs protein binders for small molecules and peptide binders for protein complexes.

Lisa Brandenburg

Visitor

Lisa is Dutch Master’s student from Utrecht University interested in biochemistry and all things peptide/protein-related.

Ljubica Mihaljevic, PhD

Postdoc

Ljubica is designing transmembrane proteins that function as biosensors.

Long Tran

Grad Student

Lukas Milles, PhD

Postdoc

Lukas is designing robust protein folds as well as intra- and intermolecular isopeptide bonds.

Magnus Bauer, PhD

Postdoc

Magnus is exploring the design of kinases and protein-based inhibitors to decode and manipulate cellular logic.

Marc Exposit

Grad Student

Marc is interested in protein design approaches that combine scaffold generation with the binding of a target of interest.

Marti Rae Tooley

Grad Student

Marti is using de novo protein assemblies and high-avidity nanoparticles with antigens to generate long-lasting vaccine responses.

Matthias Gloegl, PhD

Postdoc

Matthias is designing novel antiviral inhibitors, immunomodulators, and vaccines.

Meg Lunn-Halbert

Grad Student

Meg is working to improve vaccine design via genetic control of glycosylation.

Mohamad Abedi, PhD

Postdoc

Mohamad is interested in designing proteins to engineer and control cellular function.

Nate Bennett

Postdoc

Nate is developing computational methods to improve the design of polar protein-protein interfaces.

Nate Ennist, PhD

Acting Instructor

Nate is designing proteins for artificial photosynthesis with the long-term goal of producing renewable fuel.

Nathan Greenwood

Undergrad

Nathan is designing protein binders to target cancer and increase our understanding of biology.

Neville Bethel, PhD

Postdoc

Neville is interested in the mechanical properties of protein assemblies.

Nicole Roullier

Research Scientist

Nikita Hanikel, PhD

Postdoc

Pascal Sturmfels

Grad Student

Pascal is developing deep learning methods for structure prediction and small molecule docking.

Patrick Erickson, PhD

Postdoc

Pat is interested in designing miniprotein therapeutics with non-canonical amino acids.

Paul Kim

Grad Student

Paul is developing machine learning methods for protein design.

Paul Kwon

Grad Student

Paul is designing protein nanomaterials for biomineralization.

Peik Lund-Andersen

Grad Student

Peik is designing proteins with redox-active metal clusters for artificial photosynthesis.

Preetham Venkatesh

Grad Student

Preetham is designing protein-based therapeutics for chronic pain and metabolic disorders

Rafael Ticzon

Lab Manager

206-685-7127

Rishabh Chowhan

Undergrad

Rishabh is designing new cell-signaling proteins for various medical applications.

Rob Ragotte, PhD

Postdoc

Rob designs protein binders for applications in infectious disease.

Robert Pecoraro

Grad Student

Robert is working on the computational design of proteins that bind specific DNA sequences.

Roberta Lucchi

Visitor

Rohith Krishna

Grad Student

Rohith is developing deep learning methods for structure prediction and design.

Russel Ault, MD, PhD

Visitor

Russel is a visiting researcher from the Children’s Hospital of Philadelphia.

Ryan Kibler, PhD

Postdoc

Ryan is designing lanthanide ion binding proteins for industrial applications.

Ryan McHugh

Grad Student

Ryan is working on structure prediction and the design of protein-nucleic acid complexes.

Sagardip Majumder, PhD

Postdoc

Sagardip is designing new transmembrane transport proteins.

Sam Pellock, PhD

Postdoc

Sam is interested in developing new experimental approaches to rapidly measure functions.

Samuel Thompson, PhD

Visitor

Sangmin Lee, PhD

Postdoc

Sangmin is interested in designing protein nanocages and complex nanostructures.

Sanjay Srivatsan, PhD

Postdoc

Sanjay is trying to deploy sequencing-based technologies to screen binders.

Sebastian Kenny, PhD

Postdoc

Kenny is designing minibinder proteins to perform targeted protein degradation for novel therapeutic applications.

Shingo Honda, PhD

Postdoc

Shingo is trying to assemble asymmetric protein oligomers based on cooperative interactions between each monomer.

Shruti Jain

Grad Student

Shunzhi Wang, PhD

Postdoc

Shunzhi is interested in designing self-assembling protein nanomaterials, including capsids, 2D lattices, and 3D crystals.

Sidney Lisanza

Grad Student

Sidney is designing proteins to modulate the immune system in a predefined manner.

Stann Van-Baaren

Visitor

Stann is a visiting PhD student from École Normale Supérieure Paris-Saclay.

Stephanie Hanna

Grad Student

Stephanie is designing de novo, chemically inducible dimerization systems.

Susan Kleinfelter

Grad Student

Susana Vazques Torres

Grad Student

Susana is designing proteins that interact with small molecules and other proteins.

Ta-Yi Yu, PhD

Postdoc

‪Thomas Schlichthärle‬, PhD

Postdoc

Thomas is working to create superagonists from miniprotein binders that spatiotemporally control cell signaling.

Tim Huddy, PhD

Research Scientist

Tim works on designing proteins that are like LEGO® building blocks.

Wei (Will) Chen, PhD

Postdoc

Will is interested in building new technology that can help us understand nature.

Wei Yang, PhD

Postdoc

Wei is interested in designing protein minibinders.

Will Sheffler, PhD

Research Scientist

Will develops useful code.

William White

Grad Student

Will is using designed protein scaffolds to present antigens and co-stimulation to T-cells.

Woody Ahern

Grad Student

Xiangli Qu, PhD

Postdoc

Xiangli is interested in designing minibinders that can modulate the function of the membrane proteins like GPCRs.

Xinru Wang, PhD

Postdoc

Xinru wants to design binders that target native proteins to regulate their functions.

Yakov Kipnis, PhD

Research Scientist

Yakov is working on computational enzyme design.

Yang Bo, PhD

Postdoc

Yang Hsia, PhD

Research Scientist

Yang develops methods for designing new protein-based materials.

Yensi Flores Bueso, PhD

Postdoc

Yensi is building delivery methods for bacterial-based tumor therapies. Beyond research, she promotes diversity and equality in academia.

Yujia Wang, PhD

Postdoc

Yujia is designing de novo protein binders for protein-protein interfaces and small molecules for therapeutic applications.

Yulai Liu

Grad Student

Yulai is designing membrane proteins that can function as biosensors.

Yuliya Politanska

Grad Student

Yuliya is designing de novo DNA binding proteins with a goal of developing synthetic pioneer factors for cell fate determination.

Zhe Li, PhD

SUSTech

No Results Found