Computational Biology: Structure and Organization of Biomolecules and Cells


Stanford School of Engineering


Computational methods for investigating the structure and dynamics of biomolecules and cells play an increasingly important role in drug discovery, medicine, bioengineering, and molecular biology. Drawing from cutting-edge research, this course examines various computational techniques used to address questions around the structure of proteins, DNA, and RNA, and how their motions contribute to their function; how molecules within a cell are distributed and compartmentalized, how they move, and whether their behavior can be modified; and how structural information contributes to the design of drugs, proteins, or even cells. You will gain foundational knowledge in the use of computational analysis to extract, interpret, and combine results from experimental measurements and, in the use of physical principles, to predict structure or simulate motion.


Elementary programming background (at the level of 106A), introductory course in biology.

Topics include

  • Atomic-level molecular modeling methods for proteins and other biomolecules
  • Structure determination and prediction
  • Cellular level of spatial organization
  • Docking
  • Protein design
  • Drug screening
  • Determining structures or structural properties of macromolecular complexe
  • Cryoelectron microscopyside
  • Molecular dynamics simulation
  • Simulations at the cellular scale

Note on Course Availability

The course schedule is displayed for planning purposes – courses can be modified, changed, or cancelled. Course availability will be considered finalized on the first day of open enrollment. For quarterly enrollment dates, please refer to our graduate certificate homepage.