CHEM 731/7310-02 - NMR-Guided Molecular Dynamics
Semester: Winter 2027
Professor: S. Kalyaanamoorthy | Discipline: Biochemistry | Campus: WaterlooDescription
This course is a compact overview of theory and practice in the use of NMR-derived restraints for structure determination using molecular dynamics simulations. Due to the limited scope, it is a 6-week, 0.25-credit reading course.
Among the topics discussed are:
- Theory and Types of NMR-derived structure parameters
- Strategies for integrating NMR data in MD calculations
- Types of Software used to perform the simulations
- Planning and setup of the MD simulations
Course Objectives:
- Students will develop an understanding of the theoretical background of NMR data-driven Molecular Dynamics
- Students will gain practical experience in planning, setting up and analyzing NMR-based MD calculations
Prerequisites: Completion of Chem 731 Biomolecular NMR Spectroscopy and Chem 731 Rational Drug Design/Biomolecular Modeling: Principles, Practices, and Applications in Drug Design.
Materials
Reading material will be provided in the form of Review articles and recent research papers in the area.
Evaluation
The course grade will be based on individual paper discussions (3 discussions of 30 min, each contributes 10% to the final grade), a computational project to set up and perform an NMR-based MD using model data (30%) and one term paper assignment (40%)
Lab/Project
Rules for Group Work in Lab Assignments: All work needs to be performed by each student on their own.
Late Submissions: Late submission of the term paper will be accepted until February 9. Late submissions will have 25% of the mark deducted for each day or part of a day that the assignment is late. Assignments submitted after February 15 will receive a mark of 0%.
Schedule
- Thu: 2:30 pm - 3:30 pm in C2 278
