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

AllGraduate StudentsPostdoctoral ScholarsResearch ScientistsActing InstructorsLab ManagersVisitors

Abbas Idris

Grad Student

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

Al Nelson, PhD

Visitor

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

Alexis Courbet, PhD

Postdoc

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 reconstructing loops using equivariant deep learning models.

Andrew Favor

Grad Student

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

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.

Benedikt Singer

Visitor

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

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 Juergens

Grad Student

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

David Kim

Research Scientist

David manages the Rosetta@home distributed computing project.

David Lee

Grad Student

David is excited about understanding how cells work.

Derrick Hicks, PhD

Postdoc

Derrick is developing minibinder-drug conjugates.

Dmitri Zorine

Grad Student

Dmitri's work is centered around making switchable protein-protein interactions.

Doug Tischer, PhD

Postdoc

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

Erin Yang

Grad Student

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

Fatima Angelica Davila-Hernandez

Grad Student

Fatima is working on designing scaffolds and protein interfaces to interact with iron oxide surfaces.

Florian Praetorius, PhD

Postdoc

Florian is trying to design reconfigurable and dynamic proteins and protein assemblies.

Gyu Rie Lee, PhD

Acting Instructor

Gyu Rie is designing proteins that bind to small molecules.

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

Hernan Nunez-Ortega

Lab Manager

206-685-7127

Hojun Choi, PhD

Postdoc

Hojun is interested in designing proteins that bind to amyloid proteins and intrinsically disordered proteins.

Hsien Wei Yeh, PhD

Postdoc

Hsien Wei (Andy) is designing molecular switches to dissect complex biological systems, and biosensors to guide rapid diagnostic tests.

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 Lutz

Grad Student

Isaac is using reinforcement learning to design nanocages and peptide binders.

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 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.

Joseph Harman, PhD

Postdoc

Joseph is designing receptor agonists and synthetic receptors for cell signaling applications.

Joseph Watson, PhD

Postdoc

Joe is trying to design proteins that undergo defined conformational changes in response to different stimuli.

Joshua Lubner, PhD

Postdoc

Joshua is designing de novo protein nanoparticles that efficiently escape the endosome.

Jue Wang, PhD

Postdoc

Jue is designing functional proteins using deep learning.

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

Postdoc

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

Kandise Van Wormer

Sr. Lab Manager

206-685-7127

Kejia Wu

Grad Student

Kiera Sumida

Grad Student

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

Kirsten Thompson

Grad Student

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

Larissa Ault

Grad Student

Larissa is interested in designing proteins that can modulate and stimulate powerful immune responses.

Linna An, PhD

Postdoc

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

Ljubica Mihaljevic, PhD

Postdoc

Ljubica is designing transmembrane proteins that function as biosensors.

Lukas Milles, PhD

Postdoc

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

Marc Exposit

Grad Student

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

Matthias Gloegl, PhD

Postdoc

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

Meerit Said

Grad Student

Meerit is designing metal-binding peptides with the hopes of making them catalytically active.

Mohamad Abedi, PhD

Postdoc

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

Nate Bennett

Grad Student

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

Nate Ennist, PhD

Postdoc

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

Neville Bethel, PhD

Postdoc

Neville is interested in the mechanical properties of protein assemblies.

Nicole Roullier

Research Scientist

Nikita Hanikel, PhD

Postdoc

Patrick Erickson, PhD

Postdoc

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

Phil Leung

Grad Student

Phil is trying to make proteins that have two defined structural states.

Preetham Venkatesh

Grad Student

Preetham is currently working on designing mimics of insulin and EGF using inpainting to scaffold native interfaces.

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.

Rohith Krishna

Grad Student

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

Ryan Kibler

Grad Student

Ryan is developing a generalized method for transforming homo-oligomers into pseudosymmetric hetero-oligomers.

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 Berhanu, PhD

Postdoc

Samuel is working on the de novo design of membrane proteins.

Samuel Hendel, PhD

Postdoc

Sanaa Mansoor

Grad Student

Sanaa is using deep learning (specifically generative models) for protein structure refinement and design.

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.

Shingo Honda, PhD

Postdoc

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

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.

Stephanie Hanna

Grad Student

Stephanie is designing de novo, chemically inducible dimerization systems.

Susana Vazques Torres

Grad Student

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

Ta-Yi Yu, PhD

Postdoc

Teresa Schaaf

Research Scientist

‪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.

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 Hsia, PhD

Research Scientist

Yang develops methods for designing new protein-based materials.

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.

Zhe Li, PhD

Postdoc

Zhe is studying annealing in protein self-assembly and designing 3D protein crystals.

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