CHEM 731/7310 - Biomolecular Modelling
Semester: Fall 2026
Professor: S. Kalyaanamoorthy | Discipline: Biochemistry | Campus: WaterlooDescription
This course offers an introduction to molecular modeling and molecular dynamics (MD) simulation methods, with a focus on applications in drug discovery. Students will receive hands-on tutorials and training in using modeling and simulation software to explore a variety of research problems. Key topics include conformational analysis, molecular mechanics, and molecular dynamics; computational studies of drug-receptor interactions, docking of small organic molecules to biological receptors, and alteration of molecular structures for improvement of bioactivity.
Learning Outcomes
By the end of this course students should be able to:
| Understand the drug discovery cycle, and different concepts in drug discovery |
| Learn about different computational drug discovery methods and their usage and applications |
| Gain hands-on experience on different software programs that can be used for drug discovery applications |
| Learn the basics of programming using Unix-based commands and TCL scripts |
| Learn to perform basic molecular modelling, structure visualization, biomolecular interaction analyses, molecular simulations and their applications to drug discovery |
Materials
The students will have access to the lab computer but it is recommended that they have a laptop to allow them to work on the software that they learn in this course. All software used in this course are open source or free for academic.
Evaluation
| Component / Activity | Date or Due Date | Location /
Submission Method |
Weight (%) |
| Research Project – Report and Oral Presentation | Report Due Dec 10, 2026
Presentations: Dec 1-8, 2026 (class hours) |
Report – LEARN
Dropbox Presentation In-Person |
40% (20% report and
20% presentation) |
| Assignments/Lab Reports | First week of October and First week of November (Tentative) | LEARN Dropbox | 40% |
| Group
Discussions/activities- Literature review |
September 2026 (Tentative) | In-Person | 10% |
| Project Proposal | Oct 22, 2026 | LEARN Dropbox | 10% |
Late / Missed Content
Students are expected to submit all assignments, tests, and graded activities on time. Meeting deadlines is an important part of academic responsibility and helps ensure fairness for all students.
We understand that, on occasion, valid circumstances may prevent timely submission. In such cases, delays may be considered on a case-by-case basis, and supporting documentation may be required. It is the student’s responsibility to notify the instructor as early as possible if they anticipate or encounter such difficulties.
Unless otherwise stated, a late penalty of 5% per day will be applied to assignments submitted past the deadline, up to a maximum of 3 days. After 3 days, the assignment may receive a grade of zero unless prior arrangements have been made.
Missed tests or quizzes must be justified with appropriate documentation (e.g., medical or other official verification). In such cases, a make up assessment or an alternative assignment at the discretion of the instructor will be provided.
Please reach out early if you encounter any issues—we are here to support you within the bounds of academic policy and fairness.
Lab/Project
A research project in drug discovery (20% Presentation)
- Presentations will be held Monday, Dec 1st – Dec 8th 2026 (during class hours).
- Project Report will need to be 10-pages (max), including figures/tables but not references (20% Project Report)– Due by 10th Dec, 2026.
- Project Proposal (NSERC type) – 1 page — due by 22-Oct-2026 (10%)
- Assignments/Lab reports (2) – 40% (20% each).
- Literature Review – Group Discussion (10%) (Software/tools, CADD Papers)
Schedule
- Tue: 10:00 am - 11:20 am in C2 160
- Thu: 10:00 am - 11:20 am in C2 160
