Working at the interface of biophysics and structural biology, MCB faculty seek to understand the fundamental principles governing protein and cellular functions as well as design principles that can be exploited for synthetic biology and next generation therapeutics.
Area Directors
Area Directors help advise students about classes and rotations in their interest area. They also provide a listing of suggested courses for those interested in Biophysical and Structural Biology.
Faculty Area Directors
- Yasuhiro Arimura, Fred Hutch, Basic Sciences Division (yarimura@fredhutch.org)
- Gaurav Bhardwaj, UW, Medicinal Chemistry Department (gauravb@uw.edu)
Student Area Directors
- Elizabeth Martinez, Lee Lab (ejm45@uw.edu)
- Juliana Young, Stoddard Lab (jyoung6@uw.edu)
Suggested Curriculum
The suggested curriculum outlined below is meant to guide you in choosing classes, they are not requirements. We highly encourage you to take the Foundational courses, while the Electives are more specialized and often cross between Areas of Interest. Remember to review the UW Time Schedule for the most accurate and up-to-date information regarding whether a course is currently being offered.
2025-2026 Suggested Curriculum (document download)
BIOC 530 – Introduction to Structural Biology
Graduate-level discussion of the structure, function, and chemistry of proteins, control of enzymatic reactions. Prerequisite:a comprehensive course in biochemistry and permission.
Offered AUT, 3.0 credits, weeks 1-10. Will be offered in AUT 2025.
MCB 536 – Tools for Computational Biology
Introduction to established best practices in computational biology. Learn to organize unstructured data into standard formats, transform data for statistical analyses, and visualize the transformed data. Learn workflows for reproducible research such as version control, project organization, and code documentation. Gain basic experience with Linux command line tools and the Python and R programming languages. Classes will involve hands-on learning through coding exercises, collaborative problem solving, and extensive use of online learning resources.
Instructions: Contact graduateeducation@fredhutch.org for add code.
Offered AUT, 3.0 credits, weeks 1-10, every year. Will be offered in AUT 2025
BIOEN 588 – Computational Protein Design
Explores methods in protein engineering, emphasizing biomedical and biotechnological applications. Includes molecular visualization, homology modeling, molecular dynamics, computational protein design, and evaluation of designs. Introduces current research in subject area. Students learn to use and apply computational tools to investigate design problems.
Offered WIN, 4.0 credits, weeks 1-10, every year. Will be offered in WIN 2026.
CHEM 460 – Spectroscopic Molecular Identification
Basic theory of spectral techniques – infrared and ultraviolet/visible spectroscopy, NMR, and mass spectrometry – with emphasis on spectral interpretation skills needed for the elucidation of structure, conformation, and dynamics in organic and biological chemistry.
Prerequisite: Permission from MCB co-directors because it is a 400-level course.
Offered AUT, 3.0 credits, weeks 1-10. Will be offered in AUT 2025.
CONJ 544 – Protein Structure, Modification and Regulation
Overview of general principles of protein structure, including forces that contribute to folding and stabilization, followed by an extended coverage of the means by which protein structure and function are modified and regulated. Examples from recent developments in protein folding, processing, and allosteric regulation.
Prerequisite: Introductory biochemistry and cell biology.
Instructions: Contact graduateeducation@fredhutch.org for add code.
Offered WIN, 1.5 credits, weeks 1-5, every year. Will be offered in WIN 2026.
CONJ 545 – Molecular Interactions and Medicine
Forces governing molecular interactions in biology; with a focus on medicine. Principles of computer modeling techniques in use for predicting the molecular behavior of proteins, ligands, and their complexes. In computro ligand discovery; drug design, and the understanding at the atomic level of some genetic diseases. Two computer lab sessions.
Offered SPR, 1.5 credits. Not currently offered.
CONJ 548 – Modeling Proteins and Proteomes
Hands-on experience for modeling protein structures, using the models to predict function, and applying the prediction methods to all proteins encoded by an organismal genome. Provides an overview of protein structure, how it mediates function, and its importance for understanding protein interaction networks. Technologies involved for protein structure modeling.
Offered WIN, 1.5 credits. Not currently offered.
MEDCH 541 – Biological Mass Spectrometry
Covers the basics of modern ionization methods and mass analyzers; small molecule structure assignment, quantitative assay development by LC-MS and metabolomics; quantitative discovery-based proteomics and validation methods; and peptide sequence determination, post-translational modification mapping, and protein structure determination methods.
Prerequisite: Permission of instructor.
Offered SPR, 3.0 credits, weeks 1-10. Will be offered in SPR 2026.
PBIO 545 – Quantitative Methods in Neuroscience
Provides exposure to a variety of quantitative methods that are applicable to the study of the nervous system, and an intensive tutorial on mathematical methods and their application to neuroscience research. Format revolves around computer exercises and discussion of journal papers. Topics may include linear systems theory, Fourier analysis, ordinary differential equations, stochastic processes, signal detection theory, and information theory. Offered jointly with NEURO 545.
Offered WIN, 3.0 credits, weeks 1-10. Will be offered in WIN 2026.
PHCOL 501 – Drug Discovery and Emerging Therapeutics
Consideration of the general principles and current approaches involved in modern drug discovery and development, with an emphasis on basic concepts in drug action, delivery, and metabolism. Discussion of novel drug discovery techniques and emerging non-standard therapeutics.
Offered AUT, 2.0 credits, weeks 1-5, every year. Will be offered in AUT 2025.
Spotlight
Modeling in Seattle
Seattle is a major center for protein structure/design and structural biology. Seattle MCB faculty are leaders in x-ray crystallography, nuclear magnetic resonance (NMR), electron microscopy (EM), and small angle x-ray scattering (SAXS). Seattle MCB faculty are also at the forefront in computational design to enhance or create new protein function, and computational methods to analyze complex data sets or model single cell behavior. Visit the Institute of Protein Design to learn more about 3D protein modeling from Dr. David Baker.