This course will focus on computational techniques used to study the structure and dynamics of
biomolecules, cells, and everything in between. For example, what is the structure of proteins, DNA,
and RNA? How do their motions contribute to their function? How do they bind to other molecules?
How are molecules distributed and compartmentalized within a cell, and how do they move around?
How might one modify the behavior of these systems using drugs or other therapeutics? How can structural information and associated computational methods contribute to the design of drugs, vaccines, proteins, or other important molecules?
Computation can contribute to addressing such questions in at least two distinct ways. First, computational analysis is required to extract useful information from experimental measurements. Second, one can use computational techniques to predict structures, dynamics, and important biochemical properties.
The course will cover (1) atomic-level molecular modeling methods for proteins and other biomolecules, including structure prediction, molecular dynamics simulation, docking, and protein design, (2) computational methods involved in solving molecular structures by x-ray crystallography and cryo-electron microscopy, and (3) computational methods for studying spatial organization of cells, including computational analysis of optical microscopy images and video, and simulations at the cellular scale. The course will cover both foundational material and cutting-edge research in each of these areas, including recent advances in machine learning for structural biology.
Coursework: Students will be expected to complete three assignments, each of which will involve a combination of theoretical questions and computer work. Additionally, students will be expected to complete a project. The project will involve about as much work as an assignment, but it will be more open-ended and will allow students to delve into a topic of their choosing in more depth. Finally, students will be expected to complete an exam at the end of the quarter. More details regarding content of the exam will be released toward the second half of the quarter.
Prerequisites: Elementary programming background (at the level of CS 106A) and introductory course in biology.
Class: Tuesdays and Thursdays, 3:00 PM - 4:20 PM in Shriram 104.
Materials: There is no required textbook. We will suggest a variety of optional reading material throughout the course.
Instructor: Ron Dror
TA: Armaun Sanayei
TA: Divya Nagaraj
TA: Grace Kim
TA: Hyun Soo Jeon
TA: Tristan Saucedo
Please use Ed Discussion for questions related to lectures and assignments. If you have issues that cannot be resolved on Ed, please contact us at firstname.lastname@example.org. For instructions on how to get set up on Ed, please see the Getting Set Up handout.
All announcements will be made on Ed Discussion. For instructions on how to get set up on Ed, please see the Getting Set Up handout.
Please note that the following dates are approximate.
Submission: All assignments and the project writeup should be submitted to Gradescope.