CHEM 731/7310 - Rational Drug Design
Semester: Fall 2025
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
Readings
| Title / Name | Notes / Comments | Required | Used Versions Allowed | Price (CAD) |
| Laptop | Recommended | No |
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.
Technology
| Name of Technology | Notes / Comments | Required | URL (student access) | Price (CAD) |
| LEARN | Required | 0 | ||
| MSTeams | Required | 0 |
Evaluation
- A research project in drug discovery (20% Presentation)
- Presentations will be held Monday, 24th- Friday, 28thNovember 2025 (during class and tutorial hours).
- Project Report will need to be 10-pages (max) including figures/tables but not references (20% Project Report)– Due by 5 Dec, 2025.
- Project Proposal (NSERC type) – 1 page — due by 24-oct-2025 (10%)
- Assignments/Lab reports (2) – 40% (20% each).
- Literature Review – Group Discussion (10%) (Software/tools, CADD Papers)
Lab/Project
|
Component / Activity |
Date or Due Date |
Location / Submission Method |
Weight (%) |
|
Research Project – Report and Oral Presentation |
Report Due Dec 5th, 2025 Presentations: 24-28 November 2025 |
Report – LEARN
Dropbox Presentation – In-Person |
40% (20% report and 20% presentation) |
| Assignments/Lab Reports | First week of October and Second week of November (Tentative) | LEARN
Dropbox |
40% |
| Group Discussions/activities- Literature review | Last Friday of September and October (Tentative) |
In-Person |
10% |
| Project Proposal | Oct 24, 2025 | LEARN
Dropbox |
10% |
Schedule
- Mon: 1:30 pm - 2:20 pm in RCH 208
- Wed: 1:30 pm - 2:20 pm in RCH 208
- Fri: 1:30 pm - 2:20 pm in RCH 208
- Fri: 2:30 pm - 3:20 pm in Tutorial
