Description:
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, and how do their motions contribute to their function? 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 contribute to the
design of drugs, proteins, or perhaps even cells?
Computation can contribute to addressing such questions in at least two distinct ways. First, one can
use computational analysis to extract information from experimental measurements, and to interpret
and combine the results of such experiments. Second, one can use physical principles to predict
structure or simulate motion.
The first part of the course will cover atomic-level molecular modeling methods for proteins and
other biomolecules, including structure determination and prediction, molecular dynamics simulation,
docking, and protein design. The second part will cover techniques for determining structures or
structural properties of macromolecular complexes – for example, through cryoelectron microscopy.
The third part will cover the cellular level of spatial organization, 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.
Coursework: Students will be expected to complete three assignments, each of which will involve a combination of theoretical questions and computer work. Students will also 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.
Prerequisites: Elementary programming background (at the level of 106A) and introductory course in biology
Instructors: Ron Dror and Possu Huang
TA Office Hours are noted in the Google Calendar below.
TA: Adrian Sanborn
TA: Daniel Tang
TA: Laura Miron
TA: Meera Srinivasan
Contact:Please use Piazza for questions related to lectures and assignments.
If you have issues that cannot be resolved on Piazza, or are private issues not relevant to the rest of the class, please contact us at cs279-aut1920-staff@lists.stanford.edu.Class: Tuesdays and Thursdays, 3:00 PM - 4:20 PM in Shriram 104.
Announcements: All announcements will be made on Piazza.
Materials: There is no required textbook. We will suggest a variety of optional reading material throughout the course.
Exam: There will be a final exam held on Thursday, December 12, 2019 from 12:15 PM - 3:15 PM in STLC 111. It will include free-response questions.