INFO INST8350: Integrative Methods in Bioinformatics"
Web
http://korkinlab.org/ii8350_fa2008.htmlSyllabus
Lectures and labs:
1:00 pm - 3:00 pm
MUII conference room, Thursdays (lectures)
The lab dates and locations will be announced separately
Outline:
For the last two decades, a plethora of experimental methods to study structures of proteins, protein complexes, and the entire systems have been introduced, including X-ray crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, tandem-affinity purification, yeast two-hybrid system, site-directed mutagenesis, and others. Unfortunately, in contrast to determining structures of individual components, such as small proteins and protein domains, experimental methods have significant limitations when applied to larger macromolecular entities. To eliminate the limitations scientists employ the experimental data in the computational approaches that provide biophysical, evolutionary, and statistical data.
The main objective of this course is to introduce students to the most popular experimental methods from the point of view of the information sources that can be used in bioinformatics approaches. The key distinctive feature of this course is that students will learn not only how to use data obtained directly from the biological experiments but also how to suggest additional experiments to improve the current results. The course contains two key components: (1) the classical as well as the state of art methods will be introduced that combine experimental and computational information; (2) it will cover the usage of experimental techniques that provide information of various resolution and are applied to a wide range of biomolecular objects, from individual proteins to large biological systems, such as protein networks. Among the topics covered in this course are: experimentally restrained protein docking, large-scale protein interaction network determination, using electronic imaging data and homology modeling to obtain a near-atomic resolution structures, integrative approach towards assembly structure modeling and others.
The course will consist of lectures on the methods and their applications. Each cluster of lectures will be followed by a laboratory work, where students will have the opportunity to apply the theoretical knowledge to a number of specific problems.
Prerequisite:
INFO INST/CS 7010 (or instructor's consent). An undergraduate course in molecular and cell biology is preferable
Background reading:
Computational Methods for Protein Structure Prediction and Modeling, I and II, Ying Xu, D. Xu and J Liang, Springer: 2006
Papers for reading
The paper references will be available here.
Projects
The list of suggested topics will be available here.
Lectures
The lecture materials will be available at the MU BlackBoard
Instructor
Prof. Dmitry Korkin, PhD
Department of Computer Science
University of Missouri
207 Engineering Building West
Columbia, MO 65211
phone: +1 (573) 882-4762
fax: +1 (573) 882-8318
Office Hours : 5:15 pm - 6.15 pm M & W
Academic Dishonesty and ADA Statements:
The academic community regards academic dishonesty as an extremely serious matter, with serious consequences that range from probation to expulsion. When in doubt about plagiarism, paraphrasing, quoting, or collaboration, consult the course instructor. Cheating will result in your name submitted to the provost and no credit given for the assignment.
If you have a disability and need assistance, please notify the Access Office (A048 Brady Commons, 882-4696) or course instructor immediately. Reasonable effort will be made to accommodate your special needs.