Biophysical and Structural Biology

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

Student Area Directors

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.

2022-2023 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

MCB 536 – Tools for Computational Biology

Introduces computational research methods to graduate students in biomedical science and related disciplines. Provides a survey of the most common tools and programming languages in the field. Students will gain foundational knowledge in reproducible computational science, including workflows and code documentation, and sufficient expertise that they can continue learning relevant tools to suit specific research interests. Classes will involve hands-on learning through coding exercises, collaborative problem solving, and extensive use of online learning resources.
Offered AUT, 3.0 credits, Weeks 1-10

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, Offered every year

B STR 519 – Current Problems in Macromolecular Structure

Literature review for new topics in biological structure and macromolecules.
Offered AUT/WIN/SPR/SUM, 2.0 credits

CONJ 544 – Protein Structure, Modification and Regulation

Overview of general principles of protein structure, including forces that contribute to folding and stabilization (in week 1), followed by comparative presentation of the primary means by which protein structure and function are studied (NMR, Crystallography, CryoEM and Computational Structure Prediction and modeling) in weeks 2 through 5. The course is intended for molecular and cellular biology students without a background or ongoing research training or experience in structural analyses. The course will introduce students to the basic principles, differences and similarities between different approaches to structural analyses, and will use examples from the recent literature to learn how to evaluate and exploit such studies. Grading is based on participation, questions and answers, and a final writing assignment.
Offered WIN, 1.5 credits, Weeks 1-5, Will be offered in WIN 2023

MEDCH 528 – Biophysical Enzymology and Biopharmaceuticals

Covers in-depth treatment of chemical catalysis and transition state theory as related to enzyme mechanisms; thermodynamics and kinetics of protein-ligand interactions, protein-protein-interactions and protein-lipid interactions, and methods for their study. Discusses therapeutically relevant examples, including viruses, therapeutic antibodies, and drug targets. (
Offered WIN, 3.0 credits, Weeks 1-10, Offered even-numbered years

PBIO 545 – Quantitative Methods in Neuroscience

Discusses quantitative methods applicable to the study of the nervous system. Revolves around computer exercises/discussion of journal papers. May include linear systems theory, Fourier analysis, ordinary differential equations, stochastic processes, signal detection, and information theory.
Offered WIN, 3.0 credits, Weeks 1-10

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


Modeling in Seattle

Dr. David Baker, an HHMI investigator, displays a 3-D model of an engineered protein.

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.