Computational Structural Biology
General Course Information:
HI 6326 Computational Structural Biology UCT 1480, 5:15-8:15PM, as scheduled in Topical Outline
Instructor Information
Willy R Wriggers Office Address: 7000 Fannin, Suite 1480 Telephone Number: 713-500-3961 Fax Number: 713-500-3907 E-mail: wriggers >>at<< biomachina.org Office Hours: 2 hours before class
Reading Materials:
Required: None. (Ample reading and multimedia material will be provided for download). Recommended: 1.Cantor and Schimmel, Biophysical Chemistry: Part II: Techniques for the Study of ... (1980, W.H. Freeman) 2. Joachim Frank, Three-Dimensional Electron Microscopy of Macromolecular Assemblies (1996, Academic Press)
Course Description
This course introduces computational algorithms and data processing strategies used in modern biophysics and structural biology. The emphasis is on the algorithmic foundation and development of software fragments that may assist students in future research projects in computational biology. The course covers topics such as fast Fourier transform, computational geometry, diffraction theory, optics, and digital signal processing. The application of these methods in crystallography and image analysis of biological specimens are discussed.
Prerequisites
We will cater both to biological and quantitatively trained students. A background in at least one quantitative discipline (physics, chemistry, mathematics, computer science) at college level with solid background in geometry (ideally: vector calculus) is desirable. Knowledge of at least one programming language (ideally: C or C++) and UNIX, or willingless to acquire necessary skills.
Course Objectives
By the end of the semester, the student will have had the opportunity to meet the following objectives: Characterize the role of structural biology in concurrent biomedical research. Describe the functionality, advantages, and limitations of standard computing strategies used in processing of 3D structural data. Acquire a working knowledge of freely available software and algorithms to carry out independent research projects. Explore the possibilities for structural biology to assist in the process of determination, analyzing, evaluating, displaying, and retrieving of 3D molecular structures in a research or industry laboratory environment. Develop pieces of software and computer scripts that serve as template for own future research work.
Method of Instruction
Lectures Reading Homework Assignments Hands-On Training Sessions Group Activities
Method of Evaluation
Howework assignments 20% Take-home problem solving / programming assignment. Submissions will be done electronically with submission instructions provided at least 3 days prior to an assignment's due date. Homework projects are due at 12:00 midnight on the day indicated. Late assignments will be penalized at a rate of 5% per weekday to a maximum of 50% off, after which late assignments will not be accepted. Papers 30% Two term papers reviewing relevant literature. Paper submission per e-mail unless indicated otherwise. Papers are due at 12:00 midnight on the day indicated. Late papers will be penalized at a rate of 5% per weekday to a maximum of 50% off, after which late papers will not be accepted. Note: Submissions and paper are needed in CBE format; if not, at least one letter grade will be deducted. Check your local library and book store for a copy of "Scientific Style and Format", Council of Biology Editors, Inc., 6th ed. Cambridge University Press.
Laptop Computer Requirement
Each student must have their own computer for class. Recommended computer requirements Recommended monitor resolution: 1024 X 768 Screen Area or higher, High Color - 16bit or higher High speed line: DSL or Cable is recommended

Topical Outline

Mon 05/23/05	Session 1	Mathematical Review: Complex Numbers, Convolution, Fourier Transform	Homework 1 \| Solutions
Tue 05/31/05	Session 2	Intuitive Fourier Transforms, X-ray Crystallography Pt. I	Reading Assignment
Mon 06/06/05	Session 3	X-ray Crystallography Pt. II	Reading Assignment
Mon 06/20/05	Session 4	Synchrotron Light and Computer Practicum	Term Paper
Tue 07/05/05	Session 5	Spectroscopy, Circular Dichroism and Small-Angle-X-ray Scattering	Reading Assignment
Tue 07/12/05	Session 6	Nuclear Magnetic Resonance	Multiple Assignments
Mon 07/18/05	Session 7	3D Electron Microscopy History and Helical Reconstruction	Homework 2 \| Solutions
Tue 07/26/05	Session 8	EM Image Formation, Resolution Estimation	Reading Assignment
Mon 08/01/05	Session 9	Single Particle Reconstruction	Reading Assignment
Tue 08/09/05	Session 10	Icosahedral Symmetry Reconstruction (Virus Capsids)	Reading Assignment

Absence from any class or excuse for a late assignment or test/quiz/examination because the date is a holy day will be permissible only if the form for holy day absence, available from the Office of Academic Affairs (UCT600), has been completed by the student and the instructor, and submitted by the student to the Office of Academic Affairs within the first 15 days of the semester. Documentation of a holy day, other than well-known holy days in the community, by a religious official also is required.

Intellectual Property

Information on intellectual property issues may be found at http://www.utsystem.edu/OGC/IntellectualProperty/ippol.htm