As a graduate student in David Baker’s lab at the Institute for Protein Design, Nate developed deep learning models for the design of protein binders. Specifically, Nate developed a pipeline for the design of protein binders which uses RF Diffusion, ProteinMPNN, and AlphaFold2 to design protein binders and is easier to use, faster, and more accurate than the previous pipeline. Nate plans to wrap up a few projects as a postdoc in the Baker Lab but eventually plans to cofound a startup working on the computational design of drugs. Read More
Marti is jointly advised by Drs. Neil King and David Baker within the Institute for Protein Design. She aims to use computational methods to design new nanoparticle cages that will direct specific immune responses. Her goal is to understand more about the complex role of immunity and help generate a vaccine platform with long-lasting protection. She previously worked at Fred Hutchinson Cancer Research Center engineering B cells in their Vaccine and Infectious Disease Division. Marti holds a B.S. in Chemical and Biomolecular Engineering from the University of Tennessee. Read More
As a graduate student in David Baker's lab at the Institute for Protein Design, Sanaa is using deep learning (specifically generative models) for protein structure refinement and design. She holds a B.S. in Chemistry and Computer Science from Mount Holyoke College. Read More
As a graduate student in David Baker's lab at the Institute for Protein Design, Phil is trying to make proteins that have two defined structural states. His current approach uses helical bundles. He hopes to use these proteins as bistable switches for the applications of information storage, biological programming, and nanomachinery. He was awarded an NSF Graduate Research Fellowship in 2018. Phil holds a B.S. in Biochemistry and Genetics from the University of Minnesota. Read More
As a graduate student in David Baker's lab at the Institute for Protein Design, Fatima is working on designing scaffolds and protein interfaces to interact with iron oxide surfaces. She hopes to engineer new ways of directing inorganic synthesis of materials by understanding these molecular recognition problems. She is also interested in engineering biomaterials with properties spanning to the meso scale. She holds a B.S. in Biotechnology Engineering from the Monterrey Institute of Technology and Higher Education in Mexico. Read More
As a graduate student in the lab of biochemistry professor David Baker at the Institute for Protein Design, Brian studied the forces underlying protein folding and protein interface formation. More specifically, he designed mini-protein binders to natural targets and tested more than 100,000 proteins at the same time. After completing his Ph.D. in 2021, Brian is continuing to work in the Baker Lab as a research scientist. Read More
As a graduate student in David Baker's lab at the Institute for Protein Design, Adam expanded the residue repertoire for computational molecular design beyond the canonical 20 amino acids found in biology. Specifically, he designed new secondary structures composed of non-canonical residues with the hope that they will be broadly useful for diverse and robust molecular design. Adam completed his Ph.D. in 2021 and for now remains at IPD as a post doc. Read More
Professor Baker's research aims to predict the structures of naturally occurring biomolecules and interactions and to design new molecules with new and useful functions. Building on intial computational designs, Baker uses experiment to better understand the principles underlying catalysis and binding in order to design novel proteins and enzymes. Read More
The goal of our research is to understand how cells control the architecture of their intracellular organelle systems through the regulated self-assembly of lipid membranes and membrane-associated proteins. We employ both highly focused hypothesis tests and systems-level approaches that harness genetic, biochemical, and biophysical analytical techniques. Read More
As a doctoral student in the laboratories of David Baker in Biochemistry and Jens Gundlach in Physics, Sinduja studied synthetic biological channels for nanopore DNA sequencing and molecular diagnostics. Using de novo protein design principles, she generated diverse channel geometries and studied their ability to form pores within membranes. She also investigated the use of nanopores to study the SARS Cov-2 helicase. Sinduja is currently wrapping up projects and papers for her two labs. Read More