| Last Modified: January 4, 2001 |
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This is an introductory course designed to provide students with the background and a hands-on understanding of techniques involved in computer-aided drug design, including bioinformatics, molecular modeling, molecular simulation, docking and QSAR. Prerequisite: Consent of the Faculty. Students are expected to have some background in computers, elementary calculus, chemistry and biochemistry. |
| Lectures: | Tuesday and Thursdays 11:00 am - 12:20 pm Rm 2023 Dent/Pharm Building |
| Laboratory | Wednesday 2:00 pm - 4:00 pm Rm 4064 Dent/Pharm Building |
| Instructor: | Dr. David Wishart Rm 2123 Dent/Pharm Building |
| Contact: | ph. 492-0383 email - dsw@redpoll.pharmacy.ualberta.ca |
| TA: | Trent Bjorndahl (492-7279) |
| Textbooks: | None |
| Evaluation: | Assignments (20%) Mid-Term (30%) Final Project (50%) |
| Detailed Course Outline - 2001 |
| Jan. 9: | Introduction, examples and overview |
| Jan. 11: | Review of computers and computer terminology |
| Jan. 16: | The Human Genome Project, genes, proteins, structure |
| Jan. 18: | Bioinformatics: sequence databases and comparisons (algorithms) |
| Jan. 23: | From sequence to structure |
| Jan. 25: | From sequence to structure cont'd (databases) |
| Jan. 30: | Molecular mechanics and energy functions |
| Feb. 1: | Molecular mechanics |
| Feb. 6: | The hydrophobic effect |
| Feb. 8: | Structure comparisons & Energy minimization |
| Feb. 13: | Monte Carlo algorithms, genetic algorithms |
| Feb. 15: | Molecular dynamics, free energy calculations, simulated annealing |
| Feb. 19-23: | Reading Week |
| Feb. 27: | Small molecule structure generation - distance geometry |
| Mar. 1: | Small molecule structure generation - databases (cont'd) |
| Mar. 6: | Mid-Term Exam |
| Mar. 8: | Mid-term review, discussion of presentations |
| Mar. 13: | Dock, Autodock |
| Mar. 15: | Research, Dockvision |
| Mar. 20: | Receptor Mapping, Pharmacophore matching, deNovo design |
| Mar. 22: | Introduction to QSAR and 3-D QSAR |
| Mar. 27: | Case studies of HIV, ACE and PNP inhibitos |
| Mar. 29: | Case studies cont'd, SAR by NMR, SAR by X-ray |
| Apr. 3: | Future perspectives, miscellaneous topics |
| Apr. 5: | Student presentations |
| Apr. 10: | Student presentations |
| Apr. 12: | Student presentations |
| Laboratory Schedule |
| Date | Title | Program |
| Jan. 17: | Bioinformatics and the Internet | Netscape/Internet Explorer |
| Jan. 24: | Protein Sequence Analysis | PepTool |
| Jan. 31: | Molecular Graphics | Rasmol/Chime |
| Feb. 7: | Molecular Graphics | MolMol |
| Feb. 14: | Molecular Graphics & Evaluating Protein Structure | Swiss PDBviewer/VADAR |
| Feb. 28: | Molecular Mechanics and Energetics | Biomer-B/Hyperchem Lite |
| Mar. 7: | Lab Cancelled | Lab Cancelled |
| Mar. 14: | Small Molecule Generation and Assessment | Alchemy/QSAR |
| Mar. 21: | Molecular Docking | DockVision/SAPP |
| Site maintained by: Trent Bjorndahl |