Introduction to Biomolecular Simulations - BCH2107

Over the past four decades, 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 the energy of atoms and molecules, simulations mimic the dynamics of molecular systems across a broad range of time scales over which many interesting biomolecular events occur. As such, these molecular cartoons provide information that is 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 analyse molecular dynamics simulations on a small globular protein. Because each student will run a different simulation, they will get different results, the ensemble of which will be discussed and critically appraised by the whole class. At the end of this course, the students will have the skills to perform simulations on a protein or other biomolecular system of their choice and to read papers in the field critically.

Scheduling: 4 in-class sessions of 3 hours each, 9-12 noon

Method of Student Evaluation:
Evaluation will be based on in-class participation as well as both an in-class presentation during the 4th session and a written report on the methodology, results, and discussion of findings—due 1 week later.

Course Coordinator:
Régis Pomès

Enrollment Limit:
12