|Jan. 13||Lecture 1||Introduction to UNIX and PDB files|
|Jan. 16||Tutorial 1||UNIX, PDB files|
|Jan. 20||Lecture 2||Introduction to Molecular Modeling|
|Jan. 23||Tutorial 2a||Insight viewer module|
|Jan. 27||Tutorial 2b||Insight viewer module|
|Jan. 30||Lecture 3||Making pretty pictures - Marty Pagel|
|Feb. 3||Tutorial 3||Builder/Biopolymer module|
|Feb. 6||Lecture 4||World Wide Web Tools - Dr Gary Wiggins|
|Feb. 7||Projects||Due Date for initial Project Ideas|
|Feb. 10||Lecture 5||Databases searching and sequence alignment - Peter Kuhlman|
|Feb. 13||Tutorial 4||Databases searching and sequence alignment - Peter Kuhlman|
|Feb. 17||Tutorial 5||Homology module - 3D homology modeling|
|Feb. 20||Tutorial 6||Atomic and molecular properties|
|Feb. 24||Lecture 6||Energy minimization and dynamics|
|Feb. 27||Tutorial 7||Energy minimization|
|Mar. 3||Tutorial 8||Molecular dynamics/simulated annealing|
|Mar. 6||Tutorial 6||Atomic and molecular properties continued|
|Mar. 10||Tutorial 9||Docking|
|Mar 11-April 20||Projects||Individual Modeling Projects|
|Apr. 21||Lecture 7||Student Presentations|
|Apr. 24||Lecture 8||Student Presentations|
|Apr. 28||Lecture 9||Student Presentations|
|May 1||Lecture 10||Student Presentations|
Chemistry Room A508
(now at Monsanto)
When there is a lecture, the whole class will attend at one time. Lectures will be held in Chemistry A400 from 1.30 to 3.00 pm. Lectures will be given by Martin unless otherwise indicated above.
When there is a tutorial, the class will be split into two groups (because of the limited number of computer workstations). Tutorials will be held in Chemistry A202. One group will attend at 1.30-3.00 pm. The other group will attend 3.00-4.30 pm. Tutorials have been developed with the aim that they can be completed during these assigned times. However, occasionally you may need to complete them in your own time.
As part of some tutorials, there will be small assignments. You will be required to submit the results of these (usually Biosym folders or UNIX files) electronically.
There will be a period of several weeks in the last half of the semester when each person will be doing his/her own modeling project and there will not be regular lectures or tutorials. During this period "office hours" will be held in A202 Mon./Thurs. 1.30-4.30 pm.
During the last two weeks of the semester, there will be a series of student presentations in which you will present the results of your modeling project to the class.
The aims of this project will be: (1) to give you hands-on experience at some aspect of modeling that is more sophisticated or specialized than the introductory topics covered in the tutorials; and (2) to give you practice at using modeling to address a specific biochemical problem.
You will have to do the following:
There is no prescribed text for this class and there will be very little reading assigned. The Biosym manuals will be your most valuable source of information!
This class is not about grades. It is about learning how to do molecular modeling. If you are conscientious about doing all the assigned work and you demonstrate a high level of interest and a reasonable aptitude, you will receive an "A" grade. Just as a guideline, probably about 70% of effort in this course (outside of class times) will involve the modeling projects. The remainder will involve completion of any tutorials and assignments that you were unable to complete during class times.