Course Syllabus

Aims of the Course

Instructors:
Martin Stone
Chemistry Room A508
Email: mastone@indiana.edu
Phone: 855-6779

Marty Pagel
(now at Monsanto)

Associate Instructor:
Brandt Burgess

Course Format

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.

Individual Modeling Projects

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:

1. Choose and design your own project. This will give you experience at deciding what is a realistic modeling exercise to attempt in a short period of time. Choose a topic that is of biochemical interest to you (e.g. it might involve compounds being studied in your lab), and a project in which you will learn techniques that will be of interest to you in the future. Be careful that the proposed work can be realistically achieved in the available time (e.g. stick to relatively small molecules if possible). Martin and Marty are happy to discuss your choice with you. If you are stuck for a topic, we have a number of ideas which we have either dreamt up or been provided by other IU labs.
2. Discuss your choice with Martin/Marty no later than Friday February 7. At this stage the proposal is likely to be just a fairly vague idea but you should have in mind the biochemical questions that you are aiming to answer and the computational methods you will need to use.
3. Write a 2-3 page proposal summarizing your proposed project and submit this to Martin no later than Friday February 28. This should be formatted like a mini-grant proposal. Include brief sections on:
   • a project summary
   • the aims of the project
   • the relevant scientific background and reasons why the current project is of interest
   • the methods you intend to use to achieve the aims
   • how you intend to interpret the results
   Believe it or not, writing this paper will save you heaps of time, especially if you use it as an opportunity to learn about the techniques you will use and to come up with efficient strategies to answer your scientific questions.
4. Do the project. This will be done mostly in your own time during March and the first half of April. Martin and Marty will be available in A202 Mon./Thurs. 1.30-4.30 pm to help troubleshoot. Typically, you should expect to spend about 5-7 hours per week on your project during this period.
5. Write a 2-3 page paper summarizing the results of your project. The format of this is up to you and will depend on the project you chose. In some cases it may include a brief tutorial for the rest of the class explaining how to use a particular modeling technique.
6. Prepare and give to the class an oral presentation (15 minutes) describing your project and its results.

Reading

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!

Grades

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.