BME 220: Protein Bioinformatics
Winter 2004
MWF 2:00 - 3:10
Baskin Engineering 156
Instructor:
Carol Rohl
Assistant Professor, Biomolecular Engineering
Email: rohl@ucsc.edu
Office: Sinsheimer 220
Phone: 9-1729
Office Hours: Th 3-5; or by appointment
Catalog Description:
Covers the application of bioinformatics techniques to protein sequences and structures. Topics include protein sequence analysis, protein structure prediction, and source of experimental data. A substantial project is required.
Newsgroup: ucsc.class.bme220
Topics : (syllabus)
- review of protein structure, protein structure-function relationships
- protein classification, structural superposition, protein evolution
- experimentally determined protein structures, structure validation
- homology modeling, fold recognition, sequence alignment
- molecular dynamics
- de novo structure prediction
- potential functions, electrostatics, solvation
- sidechain packing, rotamer libraries
- optional: protein design, protein docking, function prediction, proteomics, interaction networks
Textbooks:
Protein Structure and Function
Gregory Petsko & Dagmar Ringe
New Science Press, 2002
Annual online subscriptions and a published print version are available here.
Additional reading will be taken from the primary literature and will be posted on the syllabus.
Grading:
Homeworks: 30%
Journal Clubs: 20%
Project: 50%
Journal Clubs:
Journal articles for discussion will be selected and announced prior to in class presentation and discussion. You must sign up to present a journal club article. References will be available on the syllabus.
Schedule and more information here.
Project:
This class requires completion of a individual project focusing on a problem involving protein sequence, structure, and/or function. You can select your own topic for a project, possibly related to research you are already working on, or check the list of project ideas for suggestions. More information on the project requirement can be found here.
Final versions of projects will be presented on the web here.
Online Resources:
Students are highly encouraged to explore databases and services available on the web. Check out the page of links on my homepage, or search with google.