Introduction to Biomolecular Simulations
BCH 2024H
Over the past 40 years, computer simulations have become a useful tool for the study of of biomolecular systems in a broad range of topics, including protein folding and binding equilibria and the study of enzymes, ion channels, and disordered proteins. By connecting the structure and energy of atoms and molecules, simulations mimic the dynamics of molecular systems across time scales over which many interesting biomolecular events occur. These molecular cartoons provide information difficult to access experimentally with full atomistic detail.
This course is designed as a workshop with short introductory lectures and hands-on applications. The students will set up, conduct, and analyze molecular dynamics simulations on a topic chosen by the coordinator. Students will have the opportunity to contribute to a research project in collaboration with graduate students from the Pomès lab. At the end of this course, the students will have the skills to perform simulations on a protein of their choice.
The students will be evaluated based on a report written as a mini paper describing the methodology, results, and discussion of their findings.
Course Next Offered
Fall 2019
Course Time and Location
4-day (x3hours) workshop-type course in November-December, with a hands-on workshop on days 1-3 (week 1), a follow up session of 3 hours 1 or 2 weeks later when the students present and discuss their results and analysis, and a final report due some time later.
Location:
O.I.S.E., 252 Bloor Street W., Room 5230
Nov 18-19-20, 9-12 am: three 3-hour sessions: hands-on workshop
O.I.S.E., 252 Bloor Street W., Room 7192
Nov 27, 9-12 am: follow up session: in-class discussion of results and analysis
Dec 11: final report due.
Enrollment Limit
Yes — 12
Method of Student Evaluation
Evaluations in this module are designed to provide students with the opportunity to discuss their progress on an ongoing basis. As such, the following general breakdown will be used:
20% informal presentation and discussion of preliminary results
30% presentation of analysis
20% participation in class discussions of results and analysis
30% final report
